Artin, Ma, Hjel: stop reading now.

I'm planning on using an aboleth and her slaves for my endgame! The idea is that the ley lines that crisscross this world are conduits for the vast magical power of the planet itself. They were depleted by a magical war a few centuries ago, but are replenishing themselves with the natural ebb and flow of wind and currents, just like a tired body replenishes itself with sleep. Every ~300 years on this world there is an enormous storm that engulfs the world around the equator, where the campaign continent happens to be. This storm usually serves as an outlet for the buildup of 'extra' magical force. But, since magic has been so sparse since the war, a lot of people want all the 'extra' that's built up since then.

A bunch of different factions, unknown to each other, are mobilizing to try to capture the magical flux during the Greatstorm. One of these is an ancient aboleth named Ll'brrlaw. She has a vast army of Kuo Toa (essentially skum from what I can tell), merrows, and various sea animals that she's going to use to capture Seawatch, an island at the nexus of two huge ley lines, and then perform a ritual/build a device that will allow the magic to flow through her, granting her immense power.

I know none of this is relevant to your campaign, but the point is, having telepathically-controlled slaves is great for:

-Mass organized activity, i.e. raids, seiges, etc.

-Rituals (all the aboleth's knowledge, all the life force/magic of the slaves)

-Deception, depending on how fine the aboleth's control is--could she set up a whole village full of slaves seeming to live a normal life, then lure the party there to gather information/gain their trust?

As for your underwater city, I wouldn't put more than one to three aboleth in there--they don't seem like they play well in groups. You could even have each aboleth running a different section, each of which is vastly different from the others: one with massive coral towers, one that's just a huge labyrinthine shrine to the ruling aboleth, one made of stone quarried from the ocean floor. Could be fun if each section is in conflict with the others, so the party can even run missions for one aboleth or the other.