A large part of coming up with an Adventure with either Illithids, or Aboleths is deciding what their motivations actually are. The Illithid in my game was after some where safe, with a food source and was trying to find a Chull nest to use as followers. The fact it was in the Burial Mound the PCs were looking for was simply narrative coincidence.
Illithids generally seem to want brains, slaves or knowledge - how about a single one trying to infiltrate a Library to steal something, or maybe several competing Mind Flayers all trying or the same thing. Working at cross purposes, with the possibility of the PCs maybe setting them off against one another. In the 4E background they talk about 'Brainmoss' a possible replacement for the never ending hunger for brains, which occurs only very rarely naturally, and the secret of its cultivation has been lost. Even a small patch of the stuff can draw in Illithids, making it perfect plot hook to use them. Maybe the city has a Botanical Gardens,or there's a mad Botanist that has a pot plant of the stuff. Cue psychically controlled plants, and a mad chase to get to the plant before the Illithid, or to get it back if it's stolen, or if a particularly mercenary party, an interesting bargaining session with an Illithid.
As for Aboleth's they're just weird. I've only ever used one once, and that game finished before I could reveal it. It was lurking underneath Freeport, slowly sliming the Snakemen beneath the city, and absorbing the secret knowledge in the various libraries in the cities. I stole the idea from the Laundry Files of making it an Infovore - a creature that survives on knowledge, so it was devouring the contents of the libraries and leaving the books blank. The campaign ended due to a mixture of reasons - lack of inspiration on my part, a fractious parting of the ways with a player that left a bit of a bad feeling with both me and the other GM, and that fact that the other GM in the party was also running a Freeport set game, and several of the players were getting confused over what was happening in each campaign.
Given the very Cthulhu Mythos feel to Aboleths, you could probably reskin any of several short Call of Cthulhu adventures using it, rather than whatever Mythos critter the adventure uses.