I don't Nolan is too crazy about re-casting Joker, apparentely Chris Nolan was shocked at Ledger's death and he doesn't intend to revisit the character.
Now, as far as a villain, I'm surprised it's not The Riddler, that would be the next logical conclusion considering the events of TDK.
I hope that they don't bring back Two-Face, it would be like pulling a Spiderman 3-esque plot twist out of thin air.
They already did Ra's Al Ghul, so that's the another other high profile Batman villain that I can think of. And Scarecrow.
So that would leave Penguin(doubtful), Black Mask, The Mad Hatter(doubftul), Bane and Catwoman.