Well, I think Al Ghul is definitely dead, because this version has nothing to do with the immortal comic/TAS version. Two-Face I think it's still open that he -could- come back, but due to the nature of his departure I think he is also dead.
I think Khushrenada is right on the money; Riddler is a strong possibility. It just can't be another crazy guy because we're not going to get a better psychopath than Ledger's Joker anytime soon. I could see him as a very calculating villain, playing lots of mind games, possibly not even present most of the time (think Die Hard 3 but better). Alternatively, Bane could potentially be done well. The Penguin, if anything, I think would turn up as a mob boss, a minor role like Zsasz. The Ventriloquist is similar but slightly harder to swallow. But the one that I think is almost assured is Catwoman, simply because they're probably going to want a new female lead in the next film, and she always makes for interesting interactions with Batman.