If I had to pick a villain for Bale/Nolan Combo no. 3, I'd say The Ventriloquist. He's innocent and pathetic, bullied around by this voice inside his head. Very difficult to handle since you can't just punch him, and it has the psychological depth needed for a good story. With the return of Ra's al Ghul, or Harley Quinn and the Joker, you could have a decent lineup.
Among the classics we have Catwoman, and Penguin, both of which got top-notch performances from Batman Returns. BW's take on the Penguin could be nice as a secondary character but Halle Berrie's Catwoman is a little too recent to do the character justice. Poison Ivy also needs some time to recover. Riddler, meanwhile, was handled very well in Batman Forever (except in costume) and personally I don't find his character that engaging. Perhaps a re-imagining of the character is in order since nothing's really changed in decades.
I don't see Mr. Freeze or Man-Bat coming up in this series since they're too sci-fi and not enough crime fiction for the Begins continuity. If they drastically toned down the extent of Clayface's abilities, he might be able to work.