No matter what they're going to do, it's going to be hard to top Heath's Joker. I think at the end of the filming of Dark Knight, Two-Face was supposed to be dead, but now I just don't know. It would be very comic book to bring him back and say 'Surprise.' I'm not sure whether that's a good thing.
Depp could definitely do Riddler, but I'm against Jolie as Catwoman. As others have suggested, she's far too obvious, and Catwoman herself seems a bit too obvious but perhaps necessary. They're going to need a female lead, I think it's pratically a corporate mandate. I think Eliza Dushku could do a good job, but someone less expected is needed. Talia al Ghul is somewhat boring, IMHO. Catwoman seems to fit the situation they've put Batman in better, anyway. I don't know if any of you have seen but the black man (Tiny Lister) on the ferry who threw the detonator off the boat bore tattoos similar to those of Black Mask, and some have speculated he could indeed be Black Mask.
If the theme of the next film is redemption, I say the villains should be Hugo Strange, Catwoman, and Black Mask. Hugo Strange is a psychologist and something of a notorious celebrity hired by Gordon at the Mayor's insistence to figure out the identity of and catch Batman. Meanwhile, Batman is trying to undermine a reorganization of the mafia under Black Mask while also evading the police, and, working under the radar as he must, comes into contact with Catwoman, who also has dealings with Black Mask (possibly to do with her sister, or maybe she works for him?) Anyway, Hugo Strange figures out who Batman is and blackmails Bruce into giving up the mantle. Black Mask either rapes or hurts Selina's sister and drives Catwoman to the point of killing Black Mask, and Bruce is forced to don the Batman costume again to bring in Selina and capture Strange, who, as it turns out, was behind Black Mask's getting out of Arkham and reorganizing the mob. Seems Dr. Strange has been experimenting with juicing up Arkham inmates with steroids, rendering them big angry monsters (not literally, but similar to the comics.) And, climax. Catwoman goes to jail. Batman is redeemed in the eyes of the public for exposing the corrupt Hugo Strange. Maybe Strange dies?
(One could also replace Black Mask with Riddler, or include Riddler, having Riddler betray Selina in some crime and thus driving her to seek revenge against him, perhaps him being a mastermind in with Strange. This might be a villain too many though.)
Alternatively, a good way to deal with the Joker is to show him in a cell in Arkham, hidden in the shadows. He has conversations with one Dr. Harleen Quinzel, a young psychologist trying to gain celebrity for herself by cracking the case of the Joker. Think 'Silence of the Lambs' but Harley instead of Clarice. Then remember the book ending of 'Hannibal,' how Hannibal wins over Clarice? You got it. We never hear what Joker tells Harley, in fact his silence says more than his words would, but we see her reacting, and she eventually dons her costume and stages a riot at Arkham, letting loose lots of Bat-rogues. Joker disappears in the melee, leaving a confused Harley in the path of Bats while seeking revenge against the Joker. No clue what the rest of the plot of this movie would be or who could really be the primary antagonist.
I also kind of like the original idea of Clayface- the Basil Karlo version - a crazed actor pissed they're remaking his one hit movie and so he dons the mask of the monster he played in the movie (i.e. Clayface) and starts terrorizing. Maybe he's a master of disguise. I don't know where they would really go with this other than him being a man who hides behind masks to get things done and is virtually impotent when his real face is exposed. Certainly not enough for a main plot, but he could certainly be a side plot, maybe in cahoots with someone.
I don't think more supernatural or campy villains like Poison Ivy and Mr. Freeze could really appear in the Nolan-verse, or rather I don't think Nolan would use them without substantial tweaking and watering down. Ivy would no longer have poison blood and green skin but would be an eco-terrorist poisoning industrialists who are hurting the environment who perhaps targets Bruce Wayne. Freeze would be Dr. Victor Fries, a cryogenics specialist whose wife is thought to have died of a disease but is secretly on ice while he raises capital to conduct the necessary research to cure the disease. Ivy would translate better than Freeze, but both would essentially be shells of their comic book selves and thus I think useless. Same for Bane really - I don't see anything he could provide that someone like Hugo Strange or Black Mask couldn't, with a greater degree of credibility for them. Mad Hatter or the Ventriloquist could work if taken seriously, but either one verges very closely on camp. A Calendar Killer could work well, too, methinks.
In any case, I would really enjoy seeing the Penguin played by Toby Jones, probably only in a support role. I really dislike the idea of Philip Seymour Hoffman. Have him running the Iceberg Lounge and be an informant to both sides, really in for himself. Play up the idea of him as a wannabe gentleman to accentuate the idea of Batman as outcast.
Ultimately, the deciding factor on whether or not the next Batman movie does well or at least provides a successful dramatic follow up to the Joker is tied to how closely the villain ties to Batman's own personal journey. I think we are forced to go with Catwoman and Hugo Strange/Riddler and/or Black Mask.