There's definitely a lot of possibility in the chuul invasion idea, but why limit the primary antagonists of the setting to just one type of monster? Personally, I've always been convinced that all of D&D's major aberration-type critters--illithids, beholders, aboleths, etc.--all came from the same alternate dimension (maybe something Far Realm-ish, maybe just an alternate Prime Material).
So what if the chuul incursion and terraforming (un-terraforming?) is all just the beginning? Maybe there are mindflayers and such running the show, just waiting for the chuul to prepare the environment and set up the gateways to let the real invasion in? And, along with the invaders, we get all manner of alien pest animals: rust monsters, cloakers, gricks, otyughs, and all those other very alien-looking dungeon-dwellers.
Meanwhile, the more traditional--and terrestrial--D&D "monsters" end up helping out against the invasion. Orcs and goblins and such will forget how much they hate humans pretty damned quickly when they get pushed out of their caves by a flood of aberrations. Hell, they could be PC races, even. Why bother with half-orcs when you can have orcs?
Just for kicks, maybe some type of magic could be tied into the invasion, too. Like, maybe people couldn't use arcane magic until the chuul gateways started letting weird energies into the world, or maybe psionic abilities only occur into people who've been experimented on by illithids.
As much as people will say a campaign setting should have a place for everything in it--and that's undebatably part of why Eberron won the setting search--I think one of biggest flavor-defining factors of a world is what is doesn't include. Personally, I'd like to get rid of divine magic, or demihumans, or maybe the undead, but I know that's a hard sell.
EDIT: Damn, beaten to half my ideas by Stormborn!