About becoming a mindflayer... the Emperor basically tells you this because you have to think like a mindflayer in order to defeat the brain. But why would I trust him? He claims to be your protector. But in reality he's only there to make sure that the one who really protects us (Orpheus) stays in his prison.
When we first run into the brain, we can't control it. But Tav is doing this alone. They could have played into that. Because we have these powers to link our minds with our companions. When we free Orpheus he could suggest linking our minds to become one and he would be there to protect us. Tav could be the catalyst and depending who you have with you in your party they could have played into their individuality. For instance, the party would feel the determination of Lae'zel, the sense of duty of Wyll, the fire and freedom of Karlach, etc. And by linking them with Orpheus' protection the brain would become weak enough to fight.
I don't know what you think, but this would have been a much more satisfying end for me.
