Well, there are things I love throughout all of these years, but you'll see which one is my favorite at the bottom of the list.
2001- The story was simple yet edgy. It was easy to be sucked into and the characters, while simple, were endearing and memorable. The sets were great, both in quanty and quality. The Toa, Turaga, Mctoran, Rahi, and a plethora of combiner models really fleshed out the LIFE of Bionicle's world in a very short span of time. Overall, for a line that needed to make a good first impression, this did more than that.
2002- The story ws... okay. It introduced us to elements that we couldn't comprehend at the time, yet would brilliantly come into play in later years. When the Bohrok say "clean it all", they're essentially trying to wash Mata Nui's face. But hey, there was no way for us to know that at the time. In terms of sets, the Bohrok were VERY cool and innovative, still some of the coolest villain sets to this day. The "titan" sets were cool, and the Toa Nuva at the end of the year were just great.
2003 was... eh. There are things I love about this year, but I just think some things were kind of out there. However, in terms of SETS, it was a great year. The Rahkshi were, like, the coolest things ever at the time, and some still kinda sorta include the Toa Nuva since there were released SOOOOOOOO late in 2002... in which case, yeah, more great sets.
2004... we'll get to that in a little bit.
2005- This year had some small things that I feel were necessary, but on the whole, I don't like this year that much... in terms of story or sets. While this did stand out ats the darkest year up to that point, a lot of things felt more than a little forced. As for the sets, the Visorahk were pretty cool, but the titans were just okay and the Toa hordika were... blegh.
2006- Now THIS was a great year. The story were really going somewhere, now. The scope of the universe was expanding at a downright explosive rate, and there was this crazy feeling that we really were venturing into new territory and couldn't be prepared for ANYTHING that would come our way, which would only INTENSIFY throughout the next two years as they continue to relentlessly build up more and more momentum. The Piraka, as some have said, were actual CHARACTERS, and while the story was, at times, even darker than 2005, there was still that good sense of adventure that had kind been missing in recent years. Having a bunch of characters we were familiar with from "the good ol' days" return didn't hurt, that's for sure. The sets were pretty great, all around. Axxon and Brutaka were REALLY cool, the Piraka were... also cool, and the Inika... oh, how we all went crazy for the Inika at the time. Not since the Rahkshi were sets so popular.
2007- This is where things, while still expanding, were starting to come together again, here and there. The tone was perhaps the darkest it ever got, mainly due to the setting, and the villains. I love the whole concept of the Barraki, of them being these ultra-uber bad dudes who'd been exhiled to and lurking in the darkest corner of the world this whole time, all the while these other stories had been going on. The situation was as tense as it would ever be, and there was no way to know how things were going to turn out. At this point, things were kinda getting out of hand, enough to turn some people away, but seeing Makuta enter the fray again helped ground the story so that old fans would stick around to find out what he'd do next, and just what he's really been up to all along, and Gali Nuva's blog also helped, showing that even after their crushing defeat in the previous year, our old heroes were still there... and probably always would be. I feel that, at this point in Bionicle's life, such elements were needed. The Barraki were great sets and... well, the Toa Mahri kinda suffered, but were still okay. The Titans were awesome, especially Maxillos (Makuta), still to this day being one of the greatest Bionicle sets in general, and the only one who could shrug.
2008- The story was great, with a sense of finality as everything came crashing together, building up to that epic revelation, not to mention the coolest setting we'd seen in a long, long time. Seeing old favorites finally return after all their side-questing in the previous year was wonderful, and having other Makuta featured as the main villains, well, it would be difficult to top that. In terms of sets, I think the first wave as solid. While I wish the Toa were more colorful, their builds, while basic, were very strong and heroic looking... like these really were the Toa in the absolute prime. The Makuta were FANTASTIC, all looking powerful, and surprisingly unique despite using the same torso. However, the second wave was REEEEALLY week. Takanuva was an amazing set, and most of the vehicles were great builds... however, the canister sets of the summer wave were just so underwhelming and... kind of hard to look at, compared to the winter wave. The Makuta was much less powerful looking, though Krika was still decent, and the Toa... yeah, buy this point, it felt like they'd completely run out of ideas. They weren't even using the overrused Inika build, then... they'd downgraded to a more Piraka-esque build, and not only were the summer wave Toa EVEN LESS colorful than the winter wave Toa, but their weaponry was less inspired and the masks were downright ugly. Overall, they were just... unappealing. I got every single canister set in the winter wave... yet I skipped the entire summer wave, saving my money for Takanuva, Jetrax T6, and Axalara T9. It was money well spent. Overall, still a great year with a strong start and a strong finish, though it got a little weak around the middle.
2009- Pretty good. I really liked this year, despite some shortcomings. The story was opening new doors while shedding light on things that, even throughout 2008, were still a mystery, and I did like the setting and culture. Seeing what our old heroes were still up to in the ongoing online serials made the transition to a new setting easier, and the new material was a strong basis for the new setting. In fact, in some ways, it had a very "back to basics" sort of feel. The sets were pretty good, though the quality really varied. I liked that they were, overall, much more colorful than in recent years, and had much more character and flair, and there were even some pretty fun new builds. The weapons were AMAAAAAAAAZING, and in my opinion, some of the most beautiful ever made. In terms of sets in general, though, there were a few bad apples... such as vastus. Still, the sets in general were good, and the vehicles were great.
Overall, I feel that 2009 gets a bad rep that's reeeally hard to justify.
2010, on the other hand... Whatever...
After that, I continued the follow the serials until they were abruptly put on indefinite hiatus.
Overall, 2004 has become my favorite year, just BAAAAARELY up there with 2001. This is where things really took off. The setting was amazingly beautiful, the story was tragic, and the sets were very good. The story was great because we got to see familar characters in a new light, struggling to save what little they could in the time they were given as they LOST THEIR ENTIRE CULTURE. The movie, City of Legends, is perhaps the only Bionicle movie that I'd call a legitimately good film, and not just a fun but goofy kid's flick or toy commercial. In terms of sets, the Toa Metru are some of my favorite Toa ever. They were much more poseable than in previous years, while still retaining what I like to call "slizer engineering", and refining it to its peak. Being both functional and BEAUTIFUL, I see the Toa Metru as the ideal halfway point between the classic Toa Mata build and the later Inika build. The Vahki were pretty cool, the Titans were memorable and fun to build, the Matoran were really cool... overall, just a great year. The quality, engineering, and artistic flair of the sets, along with the emotional weight of the movie, made this the best Bionicle year, in my eyes. I may not quite have felt that way at the time, mainly feeling... confused by the direction this was taking and where it may go from there, but still enticed, noneetheless, and I've only come to appreciate it more in time.
But hey, that's just me.