@Bethra
And Omeluum is a complete 180 from everything all the NPCs say about mindflayers, even Withers. It's very clear Omeluum is its own entity, and while the Society of Brilliance does seem to be a lawful evil organization (stealing eggs and what not from other species), it doesn't change the fact that Omeluum is everything that we're taught mindflayers are not by pretty much every other source in the game. So much story potential there that isn't given its due later.
As for changing into a mindflayer, what you said is right. At the 'ending' of the game, Larian wanted the story to go a certain way, even though through the entire game, they bent over backwards to let the player define the journey. It's strange and it pops up in a LOT of places. The writers think that it's cool we have this ambiguous or downright melancholy endings, and don't care if players want other 'options.'
Speaking of Omeluum, I honestly expected some kind of twist with him up to the very end. We know that the Emperor broke free of the Brain two times, and both times he needed external help. First it was Ansur, then the Brain itself let him go (at least it says so). So, how did Omeluum break free? I fully expected him to turn out to be an agent of some other god, or something like that. But Omeluum was just forgotten in the end.
