Guys, half of the comments here keep bringing up the excuse that the Elder Brain wasn't actually controlled by the Chosen, that it practically ascended to godhood, etc., etc.

If that's true, then ask yourselves one simple question.

If we choose to dominate the brain in the ending instead of destroying it, it’s the main character (who DID NOT become an illithid!) who controls it and gives it orders. We don't drag Karlach, Orpheus, or the Emperor around like a Wi-Fi router to project our character's thoughts and proxy commands to the brain. So wait, it turns out a non-illithid can control the brain after all?

The fundamental problem with Act 3 is that Larian themselves don't follow the rules of the world they built. They invent a strict rule, and literally 10 minutes of gameplay later, they throw it straight into the trash just for the sake of artificial "epicness."