It would surprise me at all for them to try to do a non-shitty version of Bane, Penguin, Riddler or Mr Freeze in one of the upcoming movies. Either Catwoman or Poison Ivy seem like the most likely to me, though, because they killed off Rachel Dawes and they need to insert a new love interest. And there's also dozens upon dozens of other villains who are lesser known to the general public that were never in any other movies which could be utilized.
I really don't see that coming up with a suitable villain is going to be the problem. The biggest problem will be coming up with a story for the 3rd movie that lives up to the 1st two.
I agree though, it sucks a lot that Joker can't be in another movie. I think they've shown they're smart enough not to try to recreate the Joker with another actor. So.. guess we'll have to move on. I'm looking forward to the next one already though. And this next time, I'm not gonna scoff when I found out who's playing the villain. Man do I feel dumb.