I enjoyed Batman Begins so much because it gave us a break from all of the old villains. In DK some of the old villains are brought back but I think that was okay because it shone some light on Harvey Dent/Two Face's character (I hated Tommy Lee Jones's version) and both Eckhart and Ledger did such a terrific job with the characters. But, now I'm hearing all these rumors about the villains in the third movie...I mean bringing back Penguin, the Riddler and Catwoman, are we not going to have new villains? To be honest I am kind of disappointed.
I think that now would be a good time to use Scarface as a primary villain. It would be a great way to reestablish the criminal element in Chicago Gotham, since various gang leaders were whacked or incarcerated in the last film. It's also a villain that hasn't been done, which gives a great deal of leeway to Nolan. I rather like the idea of Harley Quinn but she has never seemed to be an independent, and casting her just feels like a bad move. Possibly go with Bane as the secondary, but with his original origin of having been inspired by Batman to fight crime, fighting with the Bat due to their differing philosophy, and taking drugs to make him unstoppable. He needs to be cunning and ruthless for this to work, not a mindless brute.
Due to recent clips and fan-made videos I have seen of late, It seems to me the frontrunner of the fans is The Riddler. However, no way would Nolan do me like the comics.
Two ideas off the top of my head is the computer genius attacking Gotham from within using an army of anarchists and misguided students (think cyber-terrorism)
OR
Maybe a profiler, hired by the mayor to locate and capture the now-criminal Batman. Problem is, this guy is roughly of the same cloth as Dexter...using his skills to point the blame of others for his own crimes.