As it stands, you're not even fighting the Brain, just some mindflayers and a random mind-controlled dragon. It all just feels so disjointed and meaningless. There are no interactions between any of the characters and the only "meaningful" choice you make happens before you even go fight the brain. And even that choice - to squid or not to squid - is completely inorganic and disconnected from the rest of the game's narrative and choices so it feels like they included it at the last moment as some half-measure to add any sort of stakes to the encounter.
It's just kinda bewildering to me when people claim BG3 as this new "Gold Standard" for RPGs when one of the most important parts of an RPG (namely its story) is so utterly lacklustre. It's even a step down from Divinity Original Sin 2 and that game's main focus sure as hell wasn't its narrative.
Well, most reviews, including that made by players, are likely written when people when people are still in act one, possibly in act two. Considering the size of the game, and due to turn based combat, it's not possible to finish it that quickly.
My guess is that the emperor was supposed to be the final antagonist, who played both the party and the three chosen, perhaps in order to reassemble the regalia of Karsus, and gain complete control of both the elder brain and all the illithid. By comparison, the netherbrain doesn't even make sense as a concept of an antagonist. This genius-level intellect, who is so superior that you need an illithid to match it in power, is somehow not clever enough to get itself unstuck from a building. Thus conveniently allowing the party to climb and defeat it. Even as the building-crushing nautiloids, who could easily free it, are flying by.
