It would be great if they had Penguin or the Riddler in the third flick. Why? Because their portrayals in the Burton/Schumacher series weren't too accurate, and Nolan ought to put his spin on them.
I don't think that Nolan is gonna be too keen on killing off Batman's most potent adversary...Even if he's not brought back in a future Bat-film in this series...I just wanna see him survive, and be carted away to Arkham...Killing him would just seem- unnatural.