Honestly, I think Bionicle lends itself well to the concept of a "soft reboot." Jump forward a few hundred thousand years in the future, and you can have a completely different world, yet some familiarity and the occasional returning OG character.
Of course, you gotta continue having the world be split up into different sectors:
City, where technology has advanced beyond the previous generation. Maybe the vehicles from the Glatorian era have progressed and become a new sentient species, like robo-riders.
Jungle, where the dinosaurs and primitive tribes from Bota Magna reside.
Desert. Shouldn't exist anymore on the paradise Mata Nui made, but maybe the Element Lords moved their fight there and left it a wasteland?
And Water. Allows for a different aesthetic and greater variety between sets, like the Toa Mari were to the rest of Bionicle
As for presentation of the story, I think I'd take more of an approach like the former Star Wars expanded universe. You have a core TV and/or movie series that tells the main story of the sets, but also spin-offs and standalones based on the minor characters that can be told in books, comics, video games, etc. Similar to Generation 1, but the main story is easier to follow, and the extra material is just there for those interested. You won't get lost if you missed something.
I'd also probably make the main threat an organization rather than 1 antagonist. Although, you could still have a leader of the organization as the "big bad" that the story is building up to. That way, you have a main villain every year, in control of a group of villains, all of which can be beaten by the end of the year. And when you move on to the next year, you have another member of the organization, so it's not a total move back to square one.
Sorry for the long reply, but I always love toying with story concepts!