Nolan did keep Two-Face revolving around 2s, in the background at least, therefore it is possible that he could return.
The address he was at: Two Fifty Fifty Second
I have some ideas how the story lines for some villains could go, as well as a 'realistic' Mr. Freeze.
Batman is now Gotham's villain, therefore a villain must become Gotham's hero. I think this will be true regardless of the choice of villain. This would best be established, to me at least, with the Riddler, as a sort of Sherlock Holmes. He is adored by the public as Dent was for capturing criminals, but becomes so obsessed by the riddle he can't solve "Who is the Batman?" that he starts to lose his mind. There would be a great deal of tension between him and Gordon, who he would easily deduce is hiding something from him. Bane could also work as a sort of professional bounty hunter who is addicted to a drug that gives him a temporary adrenaline boost. He could be brilliant as himself, I believe Bane was portrayed as very intelligent in the comics, but become stupid and violent under the influence of the drug.
I think that there doesn't have to be a secondary villain, but a good choice would be a re-imagined Mr. Freeze. If they took the TAS Freeze and made some modifications he could work out to be what Two-Face was in Dark Knight.
Freeze should still be a scientist, and he should be trying to cryogenically preserve his wife. He would work for a rival of Wayne Enterprises, if they were to forgo the Riddler it could be a company headed by the character of Hush.
He is stealing company funds for his research, which would probably be military in nature. His lab is to be seized there's a fight, something spills... Etc. He takes his wife and himself into the freezer, she would have to already have been frozen, and locks it. He becomes severely frostbitten trying to make sure she survives, hence the unusual skin, his eyes would be damaged from partially freezing, and his lungs could be damaged in a way that he could only breath pure oxygen.
He equips himself with some sort of cybernetic suit, one of the military contracts, carries the oxygen with him, wears some sort of welding goggles, and then starts killing people realizing that he 'feels nothing' as he does so.
(By the way, if you think that he would look to ridiculous. Freeze frame on Batman's costume in Begins or The Dark Knight, and stare at the ears for one full minute.)
Freeze would not have a magic 'freeze ray', but could kill people by injecting liquid nitrogen or dry ice into them. Think of one of those pneumatic hypodermic needles doctors use some times. This would preserve the ice motif and be realistic.
As for Victor Fries, he should be:
1. A nerd, someone you can believe that
Nora was his first and only love.
2. Younger than he would normally be cast.
I think it would sell the insanity better. Think of a
teenager that just broke up with their girlfriend.
3. NOT AUSTRIAN. This, unlike Batman and Robin, is not a
remake of Adam West's Batman.
Sorry for the length. I've had this stuck in my head for a week.