It's a very good question. The whole Dead Three involvement with the Brain feels like an afterthrough to me (explains why none of them are developed as deeply as some things in act I, for example).
Perhaps initially story dealt with illithid invasion, without any of the Bhaal and Bane and Myrkul involvement, but then they decided to put them there, to tie the story with the bg1-2?
I think perhaps it was a mistake, as fun as their aesthetic is, Dead Three dilute the illithid mood of the plot, and since the only illithid you deal with is Emperor (weird and kind of dull guy who doesn't represent their race well), it feels like illithids take a major backseat.
It's just odd because illithids are meant to be those hyper-intelligent species, that nonetheless have a culture of their own - an evil culture, but culture. They have cities, they have art of some sort, they engage in commerce. Here, illithids are as good as zombies, and they are denied the opportunity to show themselves in their proper glory - it's only hinted at, but never shown.
But then again, I suppose a story with just illithids would be off-putting to people who craved the god-blood epic of yore, i dunno.