That's a good point. Assuming they get Nolan back, which for me is a must I could see him going in some unexpected routes with the villains. The classic Rogues Gallery is as yet, untouched, and Giamatti is on the right track IMO. Make him pathetic, not at all sexy, but disturbingly dangerous and psychotic.
I think Two-Face is the second best Batman villain over all. I really like the Liev Schrieber idea for him.
After that I think, regardless of her recent travesty, Catwoman should be considered. She was never as good separated from Batman, and given the setup, she could work very well. They have sort of set Bruce up as this loner when it comes to love, incapable of maintaining a real relationship because Bruce Wayne is just a mask for Batman. Then you introduce Catwoman, who is attracted to that side of him, and he to her. They are similar enough to be attracted to each other, but on opposite sides of the law. Could be good.
With the Joker, Two-Face, and Catwoman, I think you have all the villains you need. I think that others could make appearances ether as cameos like Mr. ZZasz, or in brief, almost henchman roles a la Scarecrow. I can't see the Penguin, Riddler, or Mr. Freeze making starring appearances in Nolan's Bat-universe.
And I wouldn't put it beyond them to use Bane. He's a great villain in so many ways, and you could sort of condense Knightfall into one film, like "Rocky III", where he falls, and we then have to see him work his way back. It would be a way to show another facet of Batman and his drive.