I guess it depends on why you want to streamline the story. I don't think the story needs significant streamlining, although there are a few parts that could be nixed due to their quality.
You can literally read the whole series in less time than it would take you to read Harry Potter or Game of Thrones. It's not a significantly long story and there are only a few parts that drag or are unnecessary.
2001-2003: I actually thought there were only three books in this era at first - Tale of the Toa, Beware the Bohrok, and Mask of Life. If you wanted to, you could stick to just these three books and never realize you'd skipped Makuta's Revenge or the great Tales of the Masks. I don't think you need to skip any of these - they're all great books (despite the disappointing Takanuva/Makuta Kohlii match), but you can totally do it. Skip MNOG II though, that sucks.
2004-2005: This can entirely be skipped by just reading the fourth book, Legends of Metru Nui. But you'd miss out on a lot of good stories, most notably Time Trap.
2004-2005 is something of a bug bear to me. On the one hand, it has heaps of great "side stories" for the Toa Metru. On the other hand, so many "side stories" slow the action down. The Darkness Below is entirely unnecessary, as all it does is expand a little bit on the lore of the Archives and introduce Krahka. I don't want to see these stories disappear, but if you're in a rush you can skip most of them.
That said, the first two books of 2004 are way too slow. Tales of the Toa introduces us to six heroes who are all doing pretty much the same thing, but by skipping between points of view it doesn't double up on content. We see Tahu break out of his canister, then Lewa explore Mata Nui, then Onua find Onu-Koro and meet a matoran, and so on and so forth. Each chapter focuses on a different character but they all move the narrative forward while developing each character. Mystery of Metru Nui sees every single Toa track down and rescue a Matoran, and Trial By Fire sees a pair of Toa collect two disks. You read a chapter, and then you read six chapters that tell essentially the same story, and it goes on forever and you get bored.
Also, Web of Shadows sucks. Vakama turns evil but it's only because he's been turned into a Hordika, thus robbing any impact him betraying his friends could have.
Nokama and Matau are boring and flat characters. It's like Farshtey said "I need a green one and a blue one. I'll make a creepy guy and a boring girl". Gali and Lewa weren't exactly the most unique characters ever written, but they had charm and personality that Nokama and Matau lack. Infuriatingly, over nine books Nokama never even tells Matau to stop being a creep, which would give both characters something resembling character development and personality, as well as teaching young readers that that ###### isn't on. I mean, kids are reading this! Young boys get the message that acting like Matau isn't completely gross and young girls get the message they should just put up with boys being sleezy.
The biggest sin 2004 commits is spending so much time in the first three books on a repetitive narrative while completely ignoring the hints the Vahki animations gave us of a Matoran rebellion. The Vahki are some of the coolest ideas for villain-mooks the series ever had, and they never get used to their potential as these overbearing law enforcers in the actual narrative. Being introduced to a rebel cell of Matoran who are convinced that Dume has changed and become too ruthless would offer a great storyline, an excuse to not drag out the same plot six times, and some foreshadowing, as well as actually using the Vahki to their full, threatening potential rather than an inconvenience to the Toa Metru.
I digress. I really love the Metru storyline but there's a lot of missed potential there.
I don't think there's any point in cutting anything from 2006-2007. 2006 has some great pacing, and the journey from Matoran through Kazahni, and then to becoming Toa, is just wonderful. While you could, in theory, cut the first book down, I don't see any narrative benefit in doing so. 2007 has some weaker themes, and the first book is a bit slow while it focuses on 6 Barraki, 5 of which have the same personality. That said, the introduction to Mehri Nui and it's Matoran inhabitants is not worth skipping. 2007 also has some of the stronger serials, being more integral to it's storyline.
You could totally cut 2008 down by a book. I don't see why you would - 2008 is the finale of the Mata Nui arc, and it's so much fun that you'd be depriving yourself, but it is mostly one big long fight between Toa Nuva and Makuta. However, it does start to introduce some questionable serials. Dark Mirror and The Kingdom introduce two great alternate universes only to drop them as soon as the reader starts getting attached to them. Destiny War has too many players and skips location too much to be anything short of confusing. Federation of Fear serves to bring back some fan favorite characters, but isn't exactly necessary. The Mutran Chronicles, at least, give us some great backstory on the Brotherhood of Makuta, and Dwellers in Darkness returns to focus on some of our favorite Toa and lead into the finale. The worst part is trying to keep all of these serials straight. They all lead into each other in different ways, skipping one means being confused about plot elements later on, and they're too short to comfortably jump between them. Brothers in Arms remains one of my favorites, focusing on a completely unimportant character and not being relevant to anything, meaning that a reader can go back and read it at will. If you want to streamline it, I'd read the Mutran Chronicles, the books, and Dwellers in Darkness. Unfortunately readers would get confused about Takanuva's new flight ability, but a minor rewrite to Swamp of Secrets can fix that.
2009 does the opposite. It's serials (and comics) are the best introduction to Bara Magna, and Tarduk remains the strongest character introduced in 2009. 2009 isn't as bad as some people think it is, but a new world with all-new characters is jarring and very off-putting, especially when we lose our mighty heroes with power over elements and magical masks. It's such an abrupt change in setting that would be forgivable if it lasted another two years. However, most fans were introduced to Bara Magna with Raid on Vulcanus, which has about 5 unlikable "heroes" with the personality of a tub of grey studs. The Legend Reborn, as a novel, is better, because Mata Nui is at least a more interesting character than most Glatorian were, but frankly it's not until we return to the Matoran Universe in the serials that the series really gets good again. Introducing the Matoran Universe inhabitants to Spherus Magna is much more exciting, and the hinted developments on Spherus Magna were great. Riddle of the Great Beings is the best story of the era, and a viewer could probably get away with only reading that, the comics, and The Legend Reborn (and Reign of Shadows, of course).