If I might put in 2 cents...
Firstly, remember he only says there's five winnable sects. There could be all of these in there somewhere, just most of them lose. All of them seem at least plausible.
One that I think could show up that hasn't come up is an all-human, anti-creation sect. It seems the natural reaction to the human-creation quarrels of the rebelion, and also works as an offshoot of Trakovites: all shaping and all shaped are outside the natural order and lead to destruction. Think about it: serviles left alone turn to mad cults, drayks beget drakons beget Unbound, creations invariably go violently rouge, and shaping, whether Shaper-permitted or through the Geneforge, is the culprit. Or, it could be humans who still want the free power of shaping for all, but still think that creations should be ted.
Everyone here seems to think the Shapers will split entirely, into radicals and moderates or whichever. I don't think so. If there are splits, it will be on the rebels side, just because they have more diversity. However, I think there could still be some minor internal conflicts, on the same level as those among rebels in geneforge 4, just not to the point of jeopardizing their unity. I say this because I can see the awesomeness of this already: Imagine a scenario like the negotiations in Quessa-Uss, only this time with the Shaper Council and with much higher stakes. I cant say what the sides would be or what decisions you'd be making, just that it will happen and it will be awesome.
I also don't think it seems to work for the Sholai to be their own sect. I'd be very surprised if they didn't show up somewhere, seeing as its a good roundabout way to end off the series. It's just that all the sects so far are based on philosophies and beliefs, not nationality. It's much more likely that the Sholai will ally with another sect, or better still, that you will have to convince this army of foreigners to fight on the side of your choice.
Last, though it's a stretch, the games are the Geneforge games, and I think maybe there could be a full sect strictly revolving around the Geneforge. Maybe some consider its effects to be a physical and mental perfection similar to divine ascension, creating a sort of 'cult of the geneforge' around the self-realized 'gods'. As another thought, being a Shaping artifact, it must have at least some biological aspects; what if the Geneforge developed sentience as a living being? Obviously these aren't that plausible, but either way I think the Geneforge will play a much bigger role in this last game.