I think The Riddler has been confirmed for this film. I want to see, to quote holy_king, "a dark and edgy Riddler." It will be an incredibly difficult character to make dark and edgy, so I look forward to having a really good actor running with it. If I had a choice, I'd pick Philip Seymour Hoffman. I think he could pull off a creepy Riddler.
As for non-Riddler things, I'd like to see Wayne Manor re-built, more of the Bat-pod, and Arthur or Lucius Fox come under threat. If any character can legitimately pierce Batman's secret identity without it being annoying, it's The Riddler, so I don't think I'd have a problem with that, though it usually annoys me when the hero is unmasked by the villain in super-hero films.