Your brain is the physical vessel of your mind. Your mind is, basically, the core essence that makes up You. The body is the means to support the mind and interact with the world. Dog/God may have seemed "separate", but as their "best" ending shows, they were just two shards of a shattered mind; still ultimately one entity. But in OWB, somehow we walk about Big MT with no mind; they say "remote control" but the attitude that Player's Brain shows towards the Player Char conclusively indicates it was not. Without the mind, the body is just an effectively vegetative biomass. How the body could be walking around Big MT without a mind to control it boggles mine.
So... talking to your brain just makes zero sense, and shattered my suspension of disbelief. How "my brain" could somehow be upset with "me" as if the two were entirely separate entities and not part of a whole just sat very poorly with me. And after the whole lobotomy bit in FO3's Point Lookout, I'd really hope that we're done with the horribly squicky brain damage caused to the player character.