Yes the endgame feels.... Weird at best IMHO.
There has to be an option to be the hero without becoming an illithid. Period.
And that the emperor sides with the netherbrain if you want to free Orpheus is just illogical beyond reason. The emperor did everything to get rid of the elder brain. Why should he have any reason to side with the elder brain and be a slave again? Is Tav a bigger threat to him then the brain? From a logical point of view its nonsense.
For me with this ending all choices that led me to the end feels like it was only an illusion that my choices matter. In the end I became what I was working against right from the start.
Don't get me wrong the game itself is really enjoyable but this ending does not fit the whole journey...