I wonder where they're going to go for a villain in the third film. There had been some talk of using the Joker in some way, and speculation about whether they would cast another actor, or just revise the Joker out of the planned story. Personally, I would be perfectly happy to see another actor in the role. The character is by definition mercurial, so it wouldn't bother me at all to see even a radically different interpretation by another actor.
Whether that happens or not, though, what villains are left in Batman's rogue's gallery that could work in the "realistic" vein these two Nolan films have portrayed? Possibly the Penguin, though not in the mutant-raised-by-zoo-penguins version from Batman Returns, obviously. The Riddler might work as a serial killer, of the type who writes taunting letters to the police; the riddles would be his way of expressing his superiority.
Beyond that, I'm afraid you start veering into Clayface and Killer Croc territory, which would be difficult to pull off in any "realistic" way. Unless, of course, they just decided to go all-out weird and have him face Bat-Mite.