Just to add to my earlier comments, I don't use mind flayers at all unless they're going to be the focus of a campaign arc. Their utter alienness and strange *creepy* evil sets them apart thematically from almost every other monster in the game.
They work well as creatures of the Underdark, but to have them as merely part of a host of races denies their power...if I had Illithids in the underdark, there would be only illithids and their slaves...they're so creepy, essentially, that they deserve to be the "stars" of a game, and trying to shoehorn them in to something else seems like it would be an insult to any other theme you were trying to present, or at the very least a distraction.
So, if I'm using mind flayers, then I am using every truly alien creature I can find. Chuul seem like they would work well, and the new illustration of the doppelganger makes them seem enough like space aliens (rather than twisted fey) that they seem like they'd make excellent slaves for mind flayers - some people are being controlled, others replaced by cunning doppelgangers, and slowly society crumbles until only the Mind Flayers have enoug power to ascend to the twisted thrones of the world.