Each Nolan Batman film has had three villains technically. Yes two were dominant but still you see my point. At minimum we most likely have one more to be revealed.
= Ra's, Scarecrow, Falcone
=Scarecrow, Joker, Two-Face
I really would not be surprised to see three again.
=Hugo Strange and Catwoman + minor appearance by another would not shock me. Perhaps Firefly
? An arsonist for hire who it could be revealed did the torching that killed Rachel.