Given the atmosphere of Batman Begins and The Dark Knight, it's not surprising that the comical Batman villains are out. They just don't fit, because these movies are playing Batman seriously rather than campy. So the Riddler would be tricky to pull off at best. Same goes for the Penguin to some degree as well. The Joker of course can be played anywhere from campy to psychotically deranged, and The Dark Knight handled it well. I don't really read comic books much, so I'm largely unfamiliar with some of the lesser or more recent Batman villains, and I really can't say who Nolan may use.
I am not sure if you can handle all of Batman's "comical" villains in a serious manner, but I can see Penguin and Riddler working.
The Riddler is a mastermind - that needs a challenge. So he leaves back clues to see where it leads him. He might even have a plan to trick his pursuers into a trap. My issue might be that he might be too similar to the Joker with that. (No matter what the Joker said, he certainly did "plan" for certain stuff to happen.)
The Penguin could be a crimelord that has risen to power after the "Joker Incident", or he could be a politician. He might gotten his nickname from his clothing and stature, and people might have long time underestimated him, until he rose to power and showed a ruthlessness (Crime Lord) or effectiveness (Politician) no one expected.
But we'll see. It looks like Nolan finally has found his story, right? That's great. I hope he manages a grand finale that can live up to our expectations . That won't be easy. It never is.
The thing is, Batman has a lot of silly enemies. More than even the Flash. The Joker is an example that started grim, was made goofy for a couple decades, and then reset back to grim. What they've turned Killer Croc into is kind of a shame.
The ones that are grim are usually among the more dull. Black Mask? Blah Mask, I says!
I would like to see one of Batman's opposite-number characters, like The Wrath, Prometheus, or Bane. It always strikes me as funny that Batman has an armory stocked with tanks and jets and submarines and so on, yet for the most part he just fights goons with pistols. By the third episode, he's well-established, so maybe it's time for him to meet someone who can fight him on his own terms.
The orignial Wrath story would work well. Another good candidate for translation would be Denny O'Neil's "Venom" story arc from Legends of the Dark Knight, which could be adapted to give us a Bane.