Unfortunately there will be no two-face in batman 3, as i was watching the dark knight and saw the transformation i thought two-face was being set up as the main story for the 3rd film, obviously that wont happen now.
At the end of the dark knight the joker says to batman "i have the feeling we will be doing this forever". I think clearly the idea was to bring the joker back at least partly for a 3rd film, obviously that will be unlikely now as i think a re-casting would cause uproar.
Having researched some of the villains from the comic book i think Black Mask would be a good one, the penguin will not happen as it does not fit in with Nolan's style. The riddler could work but it would have to be unlike anything we have seen before.
The first two films have had many little hints in them, obviously the way begins ended with the joker card told you a little bit about what would happen in the Dark Knight, early in the dark knight when talking about harvey dent, bruce wayne made some sort of reference to someone (or dent cant rememeber) being two-faced, a hint of what was to come. Thinking of this i think back to when Wayne goes to Lucius Fox requesting a new suit, he asks how it would hold up against dogs, he says something along the lines of it depenRAB on the dog, should be fine with cats though, maybe a nod to catwoman.
The other one obviously was the coleman reese character. Mr Reese (or Mysteries) possibly a link to the riddler or Coleman Reese becoming the riddler, I suppose only Chris Nolan knows.