That is the downside to trying to release the game earlier, content gets cut and workers rush to fill in the gaps to tie the story up which ultimately leads to nonsensical decisions.
The Emperor rushing off to the Elder Brain when you decide to free Orpheus was quite unexpected and out of character, it is not something that I ran into but watched it on Youtube out of curiosity.
And Omeluum would indeed have been amazing to recruit in the fight to spare anyone from turning into Mindflayers. Omeluum is looking for an alternate source of nourishment for Mindflayers, if the world falls to the Absolute, then that would potentially pause/put a stop to his research. So convincing him to join so he could continue the research should fit into his best interest.
I do not see the Emperor as a bad guy or a good guy. Just someone who is doing what benefits them the most in preserving their freedom and survival.
Another thing that confused me, is during one of the End Game cutscenes, I swear you can see the Emperor disguised as
Balduran while he kills a Mindflayer in the street, which does not make sense to me as I do not know why he did not disguise himself in a more humanoid form instead of using Duke Stelmane as his puppet. (I decided to just use YT vids I found for quicker examples
4:58 and
6:10 But I guess this does not really mean anything, just makes me confused on the whole Stelmane situation.