May be more than just one? I think it's a guarantee pretty much that we'll see multiple villains. Just like in the other two movies. Begins had Scarecrow and Ra's Al Ghul. Dark Knight had Joker, Two Face and Scarecrow for a bit too. So I'd say multiple villains are all but guaranteed.

I'm with Dark though. My vote is riddler. And my casting for Riddler? Crispin Glover.

For secondary villains, I think a few good ones would be: Deadshot, Hush (who could tie in with Riddler), Anarky or Victor Zsasz. Any of these would make good secondary villains I think (behind Riddler). And none of them have been used before (as far as I remember). Well I take that back, Zsasz was very briefly in Begins, but not used as a villain, rather just mentioned really. Though they did leave that wide open making it be known that Zsasz still remained at large (a coincidence? a clue to the future of the franchise? or merely a nod to a character from the universe for the fans?)