So the next Batman movie was at the very least confirmed for July 2012, which is around the time The Avengers is going to hit theaters, too.
Question is - who's going to be the bad guy?
Too soon to go back to The Joker and probably not a good idea to fill Ledger's shoes this early anyway. I'm sure there's someone out there up to the task, but the Joker returning doesn't exactly fit where the movie left off anyway.
So Batman is on the run from the police, having taken the blame for Harvey Two-Face's murders upon himself. So when Batman is on the run, who's a good match for the Caped Crusader?
Well, I think the mob needs to be rebuilt and there are some good cadidates there to take leadership of the mob.
Black Mask would fit in pretty well, I'd say, he's actually the current top dog leading the current crime wave in the comics, having found a way to bring all the kooks in Arkham under his control He's clever, well-connected and you could have any number of A or B list baddies working for him.
The Penguin would actually be the perfect foil for a Batman being hunted as a criminal. The Penguin loves to control the criminal underworld while playing a charitable socialite to the public. You could get some B-LIsters to work under him most of the time. Scarecrow, Zsasz and such could work for him in the money was good.
Bane would be pretty threatening. He's been a mercenary, he has a cunning mind on par with Batman and a rather interesting history. So long as they didn't take him too over-the-top the whole venom angle would work for him too. He could even be a drug lord peddling venom to the Gotham underground.
After those, well, who says Ra's Al Ghul ever really died? What if Neeson's character was just another decoy or, better, what if Talia Al Ghul took over the League of Shadows? Ra's did mention his wife's death, but never talked about his daughter. Talia can play the love interest or the villain, or both.
Poison Ivy, Mr. Freeze, Killer Croc and some of the more fantastical villains I don't see working out. This is more of a real-world Batman and they're a bit too zany for this version of Gotham. Catwoman would have to be a love interest of sorts and I don't see her playing into the next plot that well.
The Riddler really only works as a villain when Batman is the good guy, because the Riddler is there to frustrate him with clues to emphasis a detective angle to the story.