If you look at how the two previous films were structured in terms of villians, it seems Nolan will do a mixture of known villain with obscure villain.
Not saying they were obscure to the fans who have been following the comic forever, but Ra's, Scarcrow, and Falcone were pretty unknown to the general audience when Batman Begins was released. In contrast, Nolan went with the two biggest in The Dark Knight. Personally, you can't top those two guys. How do you move forward in a third film?
Personally, I think they have to be linked to Bruce Wayne and Batman for it to be the right story. Right now, if he does a mixture of known with unknown along with the villains having some connection to our guy, you could easily see Nolan doing Black Mask and Catwoman or Hush and Catwoman.
The Riddler is the wild card just because of the nature of who he his and who Nolan is as a filmmaker. With riddles and puzzles, cinematically, the Riddler falls in line with Nolan's Memento, Insomnia, and The Prestige.
I think there will be three villains in the film with the Scarecrow being the obvious third (a lengthier cameo than the Dark Knight). I just got a feeling that Hush and Catwoman are the next villains.
I also wouldn't rule out Taila just yet...but she seems like a long shot.
My one fear: Michelle Pfeifer's Catwoman. It's iconic. It's the greatest female part in the history of comic book films in cinema. I'm not saying it can't be beat but it's going to be really, really, really hard. Michelle's just owns that role, in the way Ledger now owns the Joker. How and who can top Michelle?