Well that was quite the read. Lots of really cool and interesting concepts in here. I think the destiny of the Skakdi, Toa of Sand Mazeka and the Great Beings' weird and exotic weapons like the Mind Spider are among my favourites. I appreciate you not shying away from the crazy power scaling in Bionicle, what with the frequent use of kraata powers, psychic mind battles, pocket suvas and more. And wow, there was no shortage of deaths either. I found the Whatever factories very disturbing. I think I'll be making much of this my headcanon for the story post-2010 save for a few small things.
As for critiques I would've liked the ending to be a bit longer, to hear more about the state of Spherus Magna and the fates of various characters - as we didn't really get much in that regard beyond a few lines on Lewa and Sahmad. Reunions between Norik and Varian and as another has said, Vakama and Lhikan would've been nice too. Just more closure like that would've made the ending more satisfying. At a few earlier points throughout the story (especially during the war) I also felt the current status of some characters had become unclear, such as Vakama who IIRC seemed to disappear later on. To be fair though, there are so many characters and so many things going on it must've been hard to juggle them all as is. I feel the ending would've been a good time to address this somewhat.
Given what Greg said about Takanuva's planned destiny I thought he'd have some hand in bringing peace between the two sides, or be involved in the illumination or something - his ending was much sadder than I expected. I'm unsure how I feel about the illumination and all those people being killed by it, including all the Vortixx and Skrall. I'm also a little confused about the Chair of Vision, though maybe I just missed something. That whole thing was a little weird.
All in all though, I really enjoyed this. Writing something of this scope is most impressive.