That's what I thought you suggested. Sounds interesting, but the first thing I thought of was the Indoctrination Theory of Mass Effect 3. And it's not a good thing for one big reason:
The indoctrination theory was some sort of alternative explanation for the bad writing bits of Mass Effect 3 (I doubt anyone would have thought of this theory if the game's story was able to deliver a satisfying conclusion). I just don't think Larian are clever enough to pull off something like that. The good news is that we don't know yet either way.