Riddler, Catwoman, and Bane are the best bets. Most folk with significant superpowers are unlikely. Bane's only "powers" are that he does lots of drugs and is really really strong. He's also solidly grounded in Batman's later years, though; as much as Nolan likes Millar's notes now and then, I've heard he wants to stick to pre-Silver Age Batman.
And due to that, Bane is doubly unlikely, because you'd need Knightfall to do him (or what would be the point?) and Robin isn't even likely, much less already poised to take over for an hour.
If we want to get creative with redoing villains, and they wanted to do more with Joker in the next movie, you could pull an interesting replacement. It wouldn't be nearly as charming as the character's ever been, but a strung-out, smeared-makeup successor could be done as Harley.
A really scary Harley that we haven't really seen before.
It'd pretty much not be Harley at all, and just be a name-drop that lets them safely bring back Joker (as a girl), but it'd work better than the Penguin or whoever the hell is left at this point.