I think the bit with Ansur when we finally see him, he should acknowledge his naivety. Because as a player, especially one that doesn't know much about the lore I kept getting conflicting information and I thought it was going to be clarified but it never was.
Ansur should have said a shade of Balduran killed him, the real Balduran is dead and he was too stupid to realize it.
Then we would need Withers explain to us why Ansur's soul stuck around and tell us Mindflayers are soulless one more time and really drive that point home.
So in one of the endings if we become a mindflayer it is clear, our character is dead and we are operating their murder still running on old memories. Or at least let us know the soul loss is a delayed process... i dont know its just all confusing and it sucks the joy out of the ending because I dont understand the stakes.
Having Ansur acknowledge his naivete would be nice!

Like @Alaric and @RoseL I think it's good evolution of the lore. The mind flayers were really designed for the Spacejammer setting and they seem much more like aliens than, say, vampires despite the mechanical similarity between the two monsters.
(By mechanical similarity I mean both reproduce by corrupting others and the corruption ruins the soul - turning to evil in the case of the vampire)
I think soul destruction was needed because WotC is "downplaying" and likely eliminating alignment. And if you don't turn to evil you need to know that this is transformation with consequences. And without Bane's revelation the Absolute plot makes little sense . . .
When I was playing EA I was most worried about how Larian would deal with the lore - ironically, I think Larian has done a great job with the lore and WotC is the one screwing up. As I keep saying the game is like a good junk shop - the main story is a shambles but if you root through the junk you find some amazing things.
Now where I agree with you completely is that the end game just sucks - there should be a way to avoid becoming a mind flayer otherwise your victory feels like a defeat. And Larian has a pretty easy way to do it:
Orpheus: " . . . . yes, but the ghaik was never had access to my full power. Even in my stupor I was able to resist The Emperor. If we can get to the brainstem I can subdue the Elder Brain long enough for you to take control of the crown."
easy peasy
But they also need to work on the entire relationship with the emperor. Any path other than "I trust you guardian, let me slurp up all these tadpoles" isn't supported. The Tav who realizes that they are being manipulated by an evil monster comes across as a petulant child "you disgust me" "I will kill you when I get a chance" The Emperor on the other hand gets some good lines.
The end game just sucks and needs to be changed.