PC -
Here's an idea to throw into the idea cauldron.
I picked up the DRACONIC LORE book by Fantasy Flight, and one of the dragons detailed is the cthonic dragon: basically, a normal dragon that was taken by the mind flyers as a baby dragon, and an illithid tadpole was injected into its brain, turning it into a dragon/illithid crossbreed-type thing - truly nasty.
Which set off big bells for me. I've always loved mind flayers, but their current status as second fiddle to drow has irked me a bit. But this introduces a cool spin to the critter: what if a mind flayer is created, not born? What if illithids capture slaves, and use them not just as slave labor, but take the best and the brightest, inject a tadpole from the main brain into them, and thus propigate the species? It would explain why they're always looking for fresh meat; not just eating brains for sustenance, but changing the brains of the best captives (and those willing & wanting to undergo the transformation) and perverting them to their side.
An illithid template would need to be created, but think of the possibilities!