how easily he joins the Netherbrain as a willing slave out of nowhere, it's nonsensical. Throughout the entire story his main prerogative is always to manipulate others to assure his freedom and continued evolution. He is even horrified when the elder brain reveals she purposely freed him so he could bait us to bring the stones to her. And then instead of seizing the opportunity to wield Orpheus against the brain if we choose to free him, since Orpheus knows an illithid is require to use the stones against it, he decides he's going to become a thrall to the brain and die fighting you instead.
The endings are so bad because it's obvious they ran out of time and had to cut so much content out of the last Act and cobble together an ending to get for release. All the talk of agency and working up factions and defeating the Chosen only to get the Mass Effect 3 treatment of pick your three colors of the same outcome, someone has to become Illithid in the end when you could have just gotten the Emperor to use the stones while Orpheus protects you from the brain's mental assault.