In Act 3 there is sooooo much content but it all feels disconnected.
While I agree with that - there's just too much stuff from unconnected quests being wrapped up here in the Lower City, so that while the location feels very authentic, the events we have there do not come together and dealing with them feels at times like working off a shopping list - that did not contribute to the sense of defeat I mentioned in the OP. That "revelation" about someone having to become a mind flayer had a singular impact.
It feels confusing, do the mindflayers have souls or not? Are they else where or am I still me? Why is killing Orphaeus or becoming Mindflayer the only options? What about Omeluum? What about other solutions? It feels so contrived and confusing.
In-world lore can be contradictory, but I would trust the information given by our resident wise old man, namely Withers, indicating that as a rule, mind flayers aren't individuals as we understand the term. Omeluum is an interesting case but he's not a problem since we can imagine that exceptions exist. The Emperor is much more of a problem. Ceremorphosis, as I understand it, appears to be not so much a process of transformation than of consumption, similar to how Alien's xenomorphs reproduce. The brains of the host bodies are consumed, so their identities should not be able to continue. I think they simply did not think that through to the end with the Emperor, given that he's a late replacement for "Daisy". As for why a mind flayer has to connect to the Netherbrain in the end, there is no in-world rationale, which is why this element comes across as wilful and nonsensical. I'm sure they had their storytelling reasons, maybe it's nothing more than they needed a reason why we could not dominate the Netherbrain right there at the final meeting in the Astral Prism. If that's the case, I would've suggested "we need to get our hands on the crown" as an alternative. But flimsy or not, almost anything would've been better having to take a form that represents what we've been fighting against.
I might add that those who want a good-ish ending while working with the Emperor almost have it worse. Because up to this final meeting in the Astral Prism, you could plausibly believe that might be possible, only to find that the Emperor's path is the evil one after all.
