This idea was explored here:
But I would be more than happy to sum up my ideas here as well.
The most immediate threat is Marendar, and, as the above post suggests, it would make a beeline right for Tuyet, due to her excess Toa Power. Since Marendar likely has some form of the power dampener that Kabrua had in The Yesterday Quest, most of the Toa will be powerless to stop it. Eventually, Marendar is defeated, primarily by Tuyet, Tahu’s Kraata powers, and the Elementally-charged Glatorian. The Yesterday Quest team may also find something important in the Great Being lab that we know they would eventually find. And that’s just the opening act.
Then, a number of large factions would be formed. The most obvious is the integrated Matoran/Agori society. Then, Velika would have his group, and he would likely be able to find some support from Matoran Universe inhabitants. Next, The Shadowed One’s group of villains would have their own goals. Finally, Tuyet would use her influence and excess Toa Power to create an army of Toa from handpicked Matoran that support her goals, and create the Toa Empire.
Perhaps that could be part of Takanuva’s super important destiny: since he has already fought a Toa Empire, he could be of use.
The other Great Beings would likely be split, with some helping Velika, some helping the Integrated Society, and some staying out. The only other loose end that I can think of is the Golden Skinned Being; each group would want him to fulfill their own dreams, so there would likely be battles fought just to get close to him. (EDIT: Also the Baterra. They’d be involved, probably just killing beings on all sides.)
Vezon would do Vezon-type things, interfering with everything everywhere. Alternately, you could do a side story where Vezon, as the only being with interdimensional travel abilities, returns all of the cured Shadow Takanuva to their own dimensions.
As for more specific, character based stuff, I think it would have been neat to see Hafu and Kapura end up doing something important in that little group they were part of, going back to the 2001 vibe of the Tohunga/Matoran being the main characters.
You could also do something cool with the Dreams Of The Mad Skakdi that are still wandering around.
One last thing, that I personally like, would be the Ignika finally becoming a true Toa: It probably isn’t happy that Mata Nui keeps taking over the mask, especially since it knows that people want Mata Nui to exist physically. Why is it fair that Mata Nui gets priority over the mask, even though the spirit of the Ignika has a greater desire to be a hero? So, with access to a Great Being lab, Artakha builds a new Toa, and the Ignika transfers its spirit to the Toa body, letting Mata Nui have the mask. And boom. Ignika, Toa of (probably) Plantlife.
(Pohatu and Kopaka’s adventure on the Red Star would remain a standalone adventure happening adjacent to all this. There is nothing important that can come from that story without invalidating an important death.)
I disagree with both of these points: I think Velika was going to become the next Teridax, in terms of being the main villain behind all of the lower villains. I wouldn’t want to see him getting a redemption arc.
As for the Turaga thing… I think the Nuva were headed in that direction. I got the feeling that they were starting to split. And I don’t just mean in terms of location: Tahu and Gali were key parts of the new society, while Kopaka expressed a desire to retire from the spotlight, even if he didn’t become a Turaga. I can’t really see the team staying together. Even if they didn’t all become Turaga, I think some of them would, like Onua.