Personally my vote goes to Catwoman/Selina Kyle, because I think there's a lot of material to mine dramatically from having her as the main villain/love interest, especially since...
- [SHOW]
- Rachel Dawes is dead.
As for possible Bat-Villians, here is a listing of many of the villiains that comprise Batman's Rogues Gallery (who have yet to appear in the new movies), with some thoughts appended:
Bane: a good Bane storyline like the one used in Batman Beyond could be an interesting side story, but I don't know if he can carry a movie by himself
Catwoman: Nolan doesn't like her, but I think she could be adapted to fit this Batverse, and provide a lot of good theater.
Mr Freeze: the backstory is great for Freeze (see the Batman The Animated Series episode "Heart of Ice" (which won an Emmy) to see why), but having things like "freeze rays" might be pushing the technology aspect too far for this set of movies. He would make a great villain IMO
Penguin: I don't know if he's as adaptable as Catwoman, and the newer takes on him are more of a "criminal mastermind" which fits in with BB and DK, but it doesn't really differentiate itself enough to be a main villain like Joker.
Poison Ivy: can't see that ever happening
Riddler: if they tone him down a bit, the idea of a hyperintelligent foe for Batman fits very well into these movies IMO. The focus has never been on over the top fight sequences, but rather outthinking the opponent with some great action sequences for good measure.
Clayface: can't see it working
Deadshot: great candidate for at least minor villain status, except for the fact that this Batman already defeated him, as depicted in Batman: Gotham Knight, the animated DVD release of six interwoven stories about Batman that are designed to take place between BB and DK. So I'd say he's out
Killer Croc: appeared briefly in Gotham Knight, and is basically a giant man-croc. Don't see that happening
Scarface/The Ventriloquist: He's pretty awesome, but I don't know if it would have the same impact over the course of a 2.5 hour movie to have the main villain be a wooden puppet. He worked well in the Animated Series, but 20 minute animated television episodes are a bit different...
If they want to go for the gold and get another villain that can hold the city hostage, and provide some great drama for the villain as well as Batman, then I'd vote for Mr. Freeze. Great backstory, and could threaten all of Gotham in a way that could allow for Batman's redemption in the eyes of the public.