Here's the pitch I've been mulling over:
We need a villain who works as a contrast to the Joker. The Joker is an anarchist, with no goal beyond destruction. This villain needs to be collected and thoughtful, with a plan that Batman has to discover. If The Dark Knight was a crime thriller, this movie would be a detective story.
Three villains pop to mind: The Riddler, Hush and the Black Mask. I vote Riddler, since a serious take on the Riddler as a cunning, sophisticated genius with a plan for getting rich/taking over Gotham/whatever. He adopts the persona as the Riddler and leaves clues because he is compulsively driven to prove his intelligence, and his riddles are a challenge against his adversary, Batman.
If the two-villain pattern is continued, Catwoman would be a great secondary villain. She continues the theme of the Batman-copies in The Dark Knight, taking on a costumed persona, but in her case it's for personal gain. Batman is troubled by her actions and hunts her down, only to be pulled into a complicated romance. He eventually becomes paranoid that the Riddler is behind his romance with her (similar to the Hush storyline) and is using her to distract him from solving the puzzle.
Since the Riddler doesn't have any disfiguring characteristics, Batman could be suspicious that anyone could be the Riddler. This would tie into an overall theme of "the power of masks" as he tries to find the Riddler and Catwoman amongst the people in his life.