I haven't finished ME3 so I don't know what shocking reveals Bharvoware has in store for me (I'm sure they're all shit), but I think that an actually interesting twist would be for the Quarian flotilla to finally cross the "Perseus veil", only to discover that their homeworld and neighboring planets are heavily populated by Quarians. Not by Geth - by Quarians, living in material prosperity and safety, but having their entire lives managed by the Geth. And preferring things this way.
Turns out, the war was never really between the AIDS Fremen and their robots, it was between AIDS Fremen who were pro-Butlerian jihad, and AIDS Fremen who were pro-AI managed society. It would also be interesting to see how an AI-run society would look like after centuries of isolation, and what kind of people it produces.