You raise some interesting points and questions. I'm a bit rusty on this subject, but I saw some possible logic errors to point out. (Or perhaps just poor wording in some cases. 
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My short answer for this is that people vary, and people tend to have temptations, and then some will fall to them. All Makuta who didn't fall to these were killed, basically. Though some like Krika were "not as horrible" as others.
Your basic theory seems to be that there was suspicion that the Makuta were evil long before it was revealed. No doubt this was somewhat true, and in a few cases like the Toa Hagah they did know earlier than most, but it apparently cannot have been widespread, due to the honest surprise shown by the Toa Metru (who previously were normal citizens in Metru Nui) when Teridax revealed himself.
At that point they had realized that the Dume they were facing cannot have been the real Dume as he was not behaving consistently with him, yet their minds did not go to the well-known local shapeshifter. This says it all -- clearly they had a deep trust in Makuta.
they are very good at playing the long game
Well, Teridax was, anyways. But then, he had some help. It was his destiny to take over the giant robot, and (so) he found out information from Tren Krom through Mutran. He learned, thus, how the long game COULD work, and fell to the temptation to try it. Besides, given that all these beings live vastly long, "long games" are not that foreign to anybody really.
Anyways, my point is, don't assume that just because one guy did who happened to be a Makuta, that is a trait of all Makuta.
"We hate you, because we cannot be you." That's the line that made me stop, despite the fact that Tahu tries to brush it off like it's just small-talk.
What is this from? Probably something from 2008? I don't recall.
Or it's also possible he just hated the makuta so much it leaked into his writing on the times before they went bad. I'm going to assume it's one of the first two.
Who are we talking about now? I'm confused. Which character spoke that line? And who are you saying hated the Makuta and leaked this into their writing?
During the Brotherhood's war with the League of Six Kingdoms, there were no reinforcements from the toa or any other group, even though the Brotherhood were fighting to free the matoran universe from the Barraki's tyranny.
I don't know where you got that idea. BS01's League page says:
The Brotherhood, having been informed of the plan by Takadox, assembled a massive army of Toa, Exo-Toa, Rahi and Rahkshi.
So basically, everyone looked at one hundred makuta against the vast armies of the six kingdoms and said, "eh, they can handle it." Granted, they were right, but this shows a level of callous hatred that borders on self destructive.
That's quite a leap, don't you think? Even if the Toa didn't help (they did), believing your uberpowerful beings capable of handling a problem, accurately, is not necessarily hatred. Hatred is something motivating something negative, often violent. This isn't there at all.
I'll grant you it could come off as callous. But you were incorrect about that. If you're referring to Matoran, they had jobs to do; they weren't supposed to be doing heroey things. That's what Toa were for.
At this point I asked, "were the makuta already hated before they went bad?"
Again, there's no reason that occasional hatred is impossible. But I see no reason to think very many, if anyone, actively hated them before they went bad.
Also, are you really talking about before they went bad or after but before they went public with this? Those are two very different things, and from pre-reading your post before I began this reply, it appears you're taking some things that happened in the second period as evidence for the first. But deceivers who are evil while pretending to be good could earn vague, gut-reaction type negative feelings from others, quite naturally. Hating someone who's actually good is a totally different thing. So those examples shouldn't really be used as evidence for a pre-bad hatred.
Also, why would they be hated before they'd done anything to earn it? Even with real racism, there's usually some bad experience with one or more actual people to fuel the Hasty Generalization that then leads to the racism. In other words, a few actually bad people that are wrongly assumed to be representative of the whole group. (Plus of course the fallacy that wrongdoing is best replied with hate, rather than forgiveness and work to improve, but that's another subject.) But you're saying they might have been hated prior to doing anything bad at all.
Why would that be so?
In "The Many Deaths of Toa Tuyet", Tuyet says she may take out the Brotherhood, even though the Brotherhood hadn't betrayed them yet and at the time Teridax was helping to defend Metru Nui against the Dark Hunters.
Foggy mem, but I presume you're talking about her final "muahahahaha--*fail*" speech. She'd been outed as evil, and the murderer of several Matoran, just prior to that speech. So we wouldn't expect her statements from then on to come from good motives that would be shared by the people of Metru Nui. She is their enemy, and as far as they know, the Brotherhood is their ally, therefore it's perfectly natural that she'd also be the Brotherhood's enemy.
And if she wants to go evil, knowing there are such superpowerful good guys helping protect the people, naturally she would be focused on them and not make a move until she found a way to become powerful enough to overthrow or at least defend herself against even them.
Instead of being even slightly confused as to why she would go after their allies, Lhikan just berates her for trying to instill her own will over a populous.
You seem to still be under the impression that Lhikan was confused as to whether she was still an ally of him and the Matoran. No, she's revealed to be an enemy, and a horrific one at that who has just murdered.
At least that's what I seem to recall. If the exact quotes would show differently we can bring them in here.
That and they don't mention him or anything about the western side of Metru Nui at any time during the story, so I can only assume that Teridax was stationed there, alone. Again displaying the same near self destructive disregard for the makuta. This isn't just thinking he can handle it, this is willful ignoring him.
You have a point here, but my guess is that Greg simply did not want to tell yet another story about Makuta for Many Deaths. And we shouldn't assume such things. Makuta seems to have played virtually no role in the normal course of events in Metru Nui, and it's not clear how often he was actually there or what he was doing when there (at least as far as I know).
During the Great Disturbance, Teridax believed it necessary to not only lock the combatants in the Onu-Metru archives, but to unleash some of the more deadly rahi on them in order to terrorize them into stopping their civil war. As we've seen from Teridax's other activities, he works in incredibly subtle ways. For him to decide that such drastic and involved measures needed to be taken, there must have been something else that guaranteed, at least in his eyes, that they wouldn't listen to him.
Another good point, but then if there was some such pre-existing hatred, distrust, or whatever against him, why the surprise at his reveal in Legends of Metru Nui?
Also, don't forget that Makuta was portrayed as preferring to work through servants including Rahi, prior to around 2007. There was an appearance of a decision made by Teridax at that time to stop doing this and to act himself. Not sure if that was merely for show as part of the Plan, but either way, Makuta using Rahi for his goals in the past perfectly fits this. What you're seeing as drastic measures to get over some imagined discriminatory closemindedness is really laziness, apparently. He didn't need them to listen to him. He had plenty of powers to stun them all (or kill if he felt it was needed due to being a war) himself.
So, you're trying to see him as a good guy at this point who had no choice, but this does not appear accurate.
Here's what BS01 says about this:
Warfare
Arguments between Matoran escalated into combat, and the denizens of Metru Nui began fighting in the streets. Work was eventually abandoned by most Matoran, and large sections of the city were destroyed during the war. The Turaga at the time was ineffective, and could not prevent the fighting.
Makuta Mutran unleashed several destructive Rahi into the city, under the cover of the mayhem.
Archives Massacre
Miserix eventually ordered his trusted lieutenant, Teridax, to halt the fighting. Teridax took a large number of the Matoran fighters and locked them in the Archives. He then released the various exhibits on the Matoran, killing a large number of them. The battle would later be known as the Archives Massacre, and put an end to the fighting. However, it gave the Makuta a very bad reputation in Metru Nui.
Notice that Mutran did something using Rahi too at this time. We have to keep in mind that the primary purpose of the Makuta to begin with was to make Rahi. It would be natural for them to think first of using them as their method of gaining their goals.
Now it did give them a bad rep, but remember that Matoran did violent things too, and there is no such hatred between the types of Matoran. And this bad rep is probably deserved.
Also, do we know at what point the majority of Makuta became evil? My sense is that due to the lack of high praise from others (not at all the same thing as discriminatory hatred; more a taking for granted), many had already become ambitious.
The BS01 Makuta page says this:
Miserix, in the wake of the Matoran Civil War, appointed each Makuta to a certain region of the universe, in order to enforce the peace in their area and prevent another uprising.
After the defeat of the Barraki, the Makuta Teridax began to develop thoughts of overthrowing the Great Spirit. After gathering knowledge from Mutran, who had obtained it from Tren Krom, he proposed the idea to the rest of the Brotherhood, the majority of which sided with him. Five Makuta remained loyal to Miserix, however, and after defeating Miserix, Teridax ordered their deaths. Miserix was secretly imprisoned on Artidax by Krika, defying Teridax's order of killing the former Brotherhood leader.
Originally biomechanical, the Makuta race eventually evolved to a state of pure energy, in which they no longer had to eat, sleep, breathe, or could feel pain. This evolution was first noticed by Bitil, and Chirox learned by examining a sample of Kojol's essence what had happened to them. Teridax ordered the Nynrah Ghosts to assist them by modifying their new armor. Soon after, the Makuta made a collective decision to shun their inner light, becoming true creatures of shadow.
So the Civil War was prior to the draining of inner light. However, is this the first time they became "bad"? No. They made a conscious choice to do that. It was no accident.
They went bad long before this, but they might not have been consciously certain about it for a while. That's often how temptation works. But at some point, probably long before Terry's takeover of the Brotherhood, most of them had probably chosen evil (whether consciously or subconsciously; they were "bad").
Likely this was prior to the Civil War. Notice Mutran's releasing dangerous Rahi but trying to hide it. It seems to me that they were already evil and intent on hiding that to some extent.
Afterwards, Teridax's actions led to makuta everywhere being even further distrusted by matoran and toa. This is the kind of behavior frequently exhibited by people attempting to justify racism.
That's a huge stretch. They're all well aware that he didn't have to release exhibits on these people and kill them. He had ways to stun them all and then imprison them, etc. In other words, it's also the reaction of good people who are not content when someone in power makes a bad call.
Yes, this could have led to racism (that one real person doing something actuall bad, leading to a Hasty Generalization), but if it did, must not have been very strong. And you started out trying to use this as evidence of pre-existing racism; that doesn't work. There is no good reason for Terry to have needed to do that.
Also, most likely with the centuries it was forgotten for the most part, as is common with politics. It may have had something to do with why he rarely seems to interact with Metru Nui since then in fact; a choice intended to help people forget by not reminding them of his existence much. Along the lines of being evil but still trying to hide it, that is, even that early.
Then when Teridax reveals his plan to the other makuta, Miserix sees it as a ploy to take control of the Brotherhood. That doesn't make any sense
Only if you make the mistake of thinking they didn't become bad until they drained their inner light, but that is false. They were already evil, ambitious, selfish, and schemers. Miserix was spot-on in seeing it as such a ploy. That was what it was. But of course, his eye was on something even bigger than merely the Brotherhood.
The Plan was to take control of Mata Nui's body, Teridax could easily leave Miserix in command of the Brotherhood if he did this.
But they'd still have to do as he wished. We saw what he was capable of in 2009 while in charge. The only reasons you didn't see similar "thought police" type activity with Mata Nui in charge was that he wasn't evil, and didn't care about what the people inside thought or did as long as they kept him operating. Had Mata Nui wanted to, he could have been the real ruler of the Brotherhood. Miserix would just be a middleman, if not a figurehead. Besides, why would not Miserix think he should be the one to takeover rather than this little upstart lieutenant? 
Meaning Teridax didn't reveal that plan, he talked to the other makuta about something else, something that Miserix saw as a threat. Then you also have to ask, why did so many of the makuta side with Teridax when their leader so openly opposed him? Teridax told them they didn't have to take everyone else's abuse.
This would make for an interesting Mirror, Mirror type alternate universe (Star Trek reference), but it's not the case. Terry did talk about what Greg said he did. See the BS01 quote above.
This, on one hand, would definitely be a threat to Miserix's station of command, as he had just been having everyone endure the hatred. On the other, wasn't he a makuta as well? Why would he disagree with Teridax's message? Because he had been dealing with the same stuff. For so long in fact that it was just the way it was supposed to be to him. Because the status quo was working and hope is scary, especially after the massive amounts of time the makuta had lived without it.
This part would be logical, but we have no evidence Terry made such an appeal. You seem to be trying to take out what he is canonically confirmed to have talked about, and using this as the replacement, but that cannot work for a theory. At best you could speculate that he made an appeal like this as a secondary thing that somehow never got mentioned canonically, but theories are supposed to have evidence.
What I see evidence for is that after the Makuta had reacted with jealousy against the people's praise for Mata Nui, they went down the evil path very early on (and any that didn't were later killed) and intentionally, and then by various means tried to hide it, and did so usually successfully, leading to widespread praise and trust. After all, why found such a revolution on jealousy if they didn't then seek what they were jealous about?
They knew they would never replace Mata Nui in the people's eyes until they did, hence the Plan, but the kind of clearly negative reactions you're theorizing don't seem to be the case. Rather, it was a lack of the top positive reaction that they were upset about -- in other words, they were selfish.
However, there -was- one thing about this that is confirmed to not be their faults; how Mata Nui tended to ignore the goings-on in here, and did not himself point to them in praise for the sake of the people. He just ignored everybody, and allowed the chance for that jealousy to crop up. In that one way, the Makuta were not entirely to blame. But this would not naturally lead to discriminatory hatred prior to being bad.
"The Brotherhood essentially said, "fine, you want us to be the bad guys, then we're the bad guys. Oh hey, what's wrong? We thought this was what you wanted us to be."
Something like this might have gone on in their twisted minds, but I doubt it was common because it doesn't really fit the situation. What they were upset about was being taken for granted, as just another part to the whole harmonious society rather than the focus of praise above all others. And this itself requires pre-existing (early-developing) selfishness, the root of evil. Nobody wanted them to be bad guys and none of them would ever honestly feel so, as I read it.
Hope this helps. 
Other replies (switching to quote marks and bold as the code won't handle that many quote tags):
"The Makuta started getting evil after they defeated the League of Six Kingdoms. Teridax realized that if THEY could do something like that there would be nobody to stop them, so Teridax overthrew Miserix, and forced all of the others to cooperate or he would kill them."
According to BS01, the thoughts of overthrowing Mata Nui happened after that; not necessarily the "started getting evil." You don't really start to plan a takeover unless you're already well down the path of evil.
"Mata Nui makes League of Six Kingdoms run by the six Barraki to conquer everybody. They end up getting corrupt. It's never stated why, but absolute power corrupts...absolutely"
Although you were probably just quoting the figure of speech for fun), absolute power does not corrupt necessarily. Mata Nui had it and remained good. The why is pretty simple -- in any varied society with freewill, you will have some who have the temptation (whether in power or out) to commit various wrongs, and you will have some of those who feel those temptations who will fall to it. It's basic statistics, really. Others, whether in power or out, will not feel those temptations, and still others will feel those temptations but turn down actually doing the wrongs because they believe in doing good.
"Teridax tells Miserix who is a good guy, causing Teridax to beat him and kill any 'good' Makuta"
I'm not so sure Miserix was a good guy. It may just be the name, implying that he was miserable by personality from the start or possibly tended to spread misery. But he also seemed kill-happy. I see him as a more gray-area type of guy, leaning good, but with his own selfish ambition and capacity for holding grudges and acting on them.
"The plan is to put the Matoran in spheres, use the Vahi to speed up time, release Matoran. Matoran will think Teridax saved them, bow down to him. The rest of the universe will follow"
I agree with this part; well said.
"6. Toa Metru interfere, and Teridax comes up with the plot to take over the robot and BE the universe. The rest is history."
No, the idea to takeover was at least as far back as Mutran's Tren Krom intel! And likely as far back as the Barraki war. It was certainly not some afterthought or Plan B. The "rest of the universe following" would be motivated towards helping them accept his takeover, likely under the guise of saving them from an unavoidable death of Mata Nui, portraying him as the rescuer who takes over only to save their lives. Then he'd get that top praise he was after from the start.
"However, you did give me an interesting idea...
What if Teridax deliberately tarnished the Brotherhood's reputation, so his brothers and sisters would be resentful and willing to aid him in his Plan? He didn't care about the other Makuta, and wouldn't care about what his subjects thought of him as long as he was in control."
Brilliant!
BTW, something I forgot to add above -- TerryMack's normally subtle approaches are things he does for his non-public, Plan-oriented, and especially his true goal-oriented actions. That doesn't apply to the Archives Massacre because that was public. So to appear hopeless inept and appealing to brutish bludgeoney strategies there makes perfect sense. If instead he showed off great judgement and nuance brilliance there, likely he would risk others realizing how clever he is and this would of course hurt his ability to manipulate subtly in the future.
(By separating the Plan from his true goals I'm talking about his killing of the Makuta who helped him get into power; they knew the rest of it, but that was something he kept totally to himself.)
So anyways, intentionally tarnishing does fit that sort of subtle thing. He would both be hiding his manipulative nature publicly, and using it at the same time, both to move public sentiment and to in turn affect his pawns, the other Makuta. Makes sense.
But yeah, there was no widespread, intense hatred of Makuta along the lines of racism.
"Look at nearly all persons you know who had and the power and the oppurtunity for absolute power. Power corrupts, like the Ring in LOTR you can't have it long and know it power before you'll get evil yourself."
Interesting analogy, but keep in mind Tolkien went out of his way to remind the reader that the Ring was not a neutral power; it itself was evil because it was made by the evil Sauron for that purpose, and basically seemed to be incrementally "downloading" an evil alternate persona into people who possessed it, leading to eventually full schizophrenia, as especially shown well in the movie version of Gollum, with the invading personality being the Ring's evil personified.
Power itself does not corrupt, despite how cool-sounding that idea makes that figure of speech. A lack of morals corrupts. And this may lead to stronger temptation when such a person has power, but it's still not really the power that is doing the actual corrupting.
"Remember, I put these in chronological order. The Archives Massacre hadn't happened yet, there was no real reason for them to have a bad reputation. And even when she was mad with power she still believed that she shouldn't attack anything that didn't present an imminent threat. Meaning she considered the Brotherhood a likely danger."
I must be misunderstanding you, as it seems we're talking about Tuyet? That was not before the Archives Massacre. Sorry if I've lost track of what we're talking about here with all these pronouns. By the time of Tuyet's murders and out, there had been countless centuries for bad reps to build up... and also for them to fade, though, as with politics.
But maybe we should get the exact quote and source name that you're talking about, to avoid any further confusion.
"Why? There's a war going on in the place he's supposed to be protecting. There's no way he'd just sit back and watch. This relates back to the fact that they are by nature selfish, an attack on Metru Nui would be a personal affront to him."
So we're not talking about Many Deaths? The DH/Toa war, maybe? What?
"The answer to that was written all over Teridax's lines and roles throughout the series. He wanted to be the important one, he wanted to be the one people looked to, he wanted to be at the top.["
So you're saying, he would have wanted to keep Miserix in charge? But how could Miserix be sure of such a thing, and how do you square that with the fact that Terry slaughtered the other Makuta, even the most loyal like Gorast?
"Abuse has many meanings. You see a child sitting in his home, he's dirty, a little bruised up, it only seems to get progressively worse as time goes on. His parents didn't do it, but they refuse to help him fix it either. That's neglect, an often overlooked form of abuse."
I hardly think an analogy of a neglected child applies to the Makuta! They're fully "adult" and they are well-more than capable of looking out for themselves.
NOTE: In part of writing the above I was under the impression due to the BS01 Makuta page that the Archives Massacre happened before the Barraki war, but the Timeline debunks that, pardon if that error crept through into the posted version anywhere, out of time to proofread, heh.
