I was thinking that perhaps Black Mask could work. Given that after Batman Begins a lot of the criminals were out in Gotham again and that the Joker messed around with the hierarchy of various gangs a bit, it wouldn't be too implausible for him to appear. I think he's probably one of the better Batman villains as well.
I'm torn on the issue of the Riddler. I like the character, but I don't really like Johnny Depp that much. Certainly feel that Depp would lend something to the character and I'm unable - off the top of my head - to name a better idea for an actor. I also quite like the sound of Ouch!'s idea for Batman working with the Penguin against the Riddler.