I had hoped that Anthony Michael Hall was being cast for Riddler. I thought he would've made a good one.
Praetor has some really good ideas. I wouldn't mind seeing that. Hopefully, Nolan will delve more into Batman's deep rogues gallery and use guys like Black Mask in the next film.
I don't think Nolan, etc. should be worried about topping Ledger's Joker. The focal point should be Batman anyway. What Burton's films did wrong was give the villians way too much focus, and Schumaker made it even worse. What made Batman Begins work was the focus on Bruce. I think they need to go back to that, and take the pressure off themselves from trying to top the Joker.
I was reading some of the comments here and I think Bane is a great villian. He combines freaky strength with a cunning mind. Even without venom, Bane was a tough, dangerous foe. If you perhaps use the ninja-like suit that was in The Batman cartoon I think Bane would be a really good villian to use. However, I don't think he should necessarily be in the third film. He works better going against a more established Batman.
Some of the villians I would like to see: Black Mask, Talia al Ghul (perhaps out for revenge because she thinks Bats murdered her father), Roland Dagget, perhaps a younger pre-Boss Zucco (merely an illusion to Robin without putting Robin in the pic), Riddler. I don't see the Penguin really carrying a movie unless he's got some support. Perhaps having a gang war between Black Mask and Penguin could be a way to involve them both in the film in a 'realistic' Nolan way.