While Dex did defeat the Complex so it would be illogical to use them as a repeat villian, it should be noted that in one ending Dex frees all of the clones. This could be used for a villian in a sequel.

Dex is supposed to be basically a super-human. Her clones are all pretty much the same, if not better. One of her clones could decide not to be Mrs. Nice and instead try to conquer the world like the Complex did.

You could even make contact with other clones, see how they turn out, maybe some decide to form a resistance. Clones assassinating clones. Lots of potential for a story and more fun.

Maybe not the best idea ever, but I love cyberpunk and it's an excuse for more game.

If you have any ideas, go ahead and elaborate. You never know maybe Dreadlocks will consider a sequel?