Nick concurs. Nick decides to refer to himself in the third person, and wishes to remind people here that he has yet to play Geneforge 3.
The Sholai are the best development of the series; they are their own isolated society, and not like a sect (of independent creations) but indifferent. What they want to do, as Masha says in the first Geneforge, is make peace and trade with other cultures. I can see the Shapers Council learning of the Sholai and deciding to seek them out and dominate their culture; supporting evidence includes the end of Geneforge, in which the Council is pleased that you wiped out the Sholai (if you did).
It's interesting how the story is open to many endings, but one must be chosen for a sequel. Also, the PC's in each game are unrelated, and they clearly have at least a few years between each game. Basically, the "chosen" plot, as I've read it, goes something like this:
The apprentice on Sucia Island returns to the Shaper Council, having destroyed the Geneforge and left each sect alive. The Council send Zakary and Barzahl to investigate, and they end up settling Drypeak (and the countless areas beyond), where the Takers and Awakened migrate. The Obeyers are either absorbed back into Shaper The (Neo) Takers eventually build another Geneforge -- suggesting that decades have passed, with all the buildings etc up there -- and nobody manages to use it. Meanwhile, Lord Whatsisface is hidden away gathering power. The next apprentice goes to the mountains and learns of all this, comes back and reports it. The Barzite ending includes domination over the Shapers, so that couldn't happen. The Awakened ending suggests diplomacy between the Serviles and Shapers. Nick forgot the Taker ending, so the assumption is that the loyalist ending works out again.
Correct me if I'm wrong?