Freeze, Ivy, Croc, Deadshot, Man-Bat and Clayface are all out of the picture. The whole idea is to make the Bat franchise more down to earth, so all of the super-powered villains won't be featured.
Deadshot and Croc have been used already in the Gotham Knights animated feature that spans the time between 'Begins' and 'TDK'.
Red Hood was in fact the Joker before he became the Joker so that's out the window, and the second Red Hood was Jason Todd, the second Robin who was murdered. Since Nolan has specifically stated that he won't have any mention of Robin in his films, Red Hood is out the window as well.
Hush's very first storyline involved him working with The Riddler to manipulate Batman's entire rogue gallery into attacking him one after the other, so without introducing all the others first, they'd have to write a completely new origin for Hush, which i see as unlikely.
Bane.... there is no valid reason why Bane couldn't be in one of these movies. You don't need a muscle bound actor to play the part, you just need a muscle bound idiot to stand in front of the camera, all the lines can easily be delivered by someone else. Anyone ever hear of Darth Vader for example? He also doesn't need to be ridiculously strong, just significantly stronger than Bats, and it's got to be as a result of drugs.
Penguin... again, no good reason why he shouldn't be in it. He's a mob boss who hides his criminal activities behind the facade of being a nightclub owner. He doesn't need to have weapons in his umbrella or even be called the Penguin by name. He's just got to be a short fat guy who waddles a lot, dresses with sophistication, and loves birds and his name be Oswald Cobblepot. They could easily have 'The Penguin' be a mocking nickname that his thugs refer to him as.
How exactly is that premise too comedic and unrealistic?
The script for TDK night actually states that Dent is seen lying at on the ground, dead. Could be redone, but why do it? What's the point in having him suddenly be alive. The occassional movie goer would be pissed off.
TDK ended with Batman being hunted by the police. The main premise could easily be that a new Mayor is elected and his primary campaign is to rid Gotham of all the psychos primarily Batman (and then they can keep bringing up the idea that Bats attracts the psychos rather than stopping them from coming). In order to efficiently hunt Batman, they hire an expert to help them answer their biggest Riddler: Who Is Batman?
And in walks Edward Nygma, detective for hire, which coincidentally, is the role that the Riddler plays now. He works with the Bat family to solve cases, make money legitimately, and generally prove his intellectual superiority over Batman (which he rarely does). So there's even plenty of material to research if they wanted to go that way.
The Mad Hatter is unlikely because his whole gimmick is using circuitry to control people's minds while having an unhealthy obsession with Alice In Wonderland. The obsession part is believable enough, but the mind control isn't.
Calender Man conducts crimes on holidays and occassions marked on the calender. Would make a decent intro villain for Bats to simply pound on in the first 10 minutes a la Scarecrow in TDK, but not a villain for the films duration.
Black Mask is another mob boss basically, so he could play the same role as Penguin.
Talia Al Guhl isn't really even a villain. Ok so she's worked with the Secret Society of Supervillains in the past and ran the League of Assassins sometimes, but she rarely does anything to hurt Batman. He is her 'beloved' after all. The same thing applies to Catwoman. Ok she's a thief, but when has she ever tried to kill Batman? All she ever does is flirt with him, and to me that doesn't scream summer blockbuster material at all.
Scarface and The Ventriloquist would be another good one to use as a mob boss. Ok people won't take an old man with a puppet as the leader of a gang seriously at first, but if they did it in a way where all the gang members were convinced that the puppet was alive, and showed Scarface to be stupidly sedistic and malicious like he is in the comics, than i think people would grow to like his character more. The best part of his character in the books is that no one, not even Batman, completely believes that the puppet isn't alive.
Other than that, i don't think there are any other villains worth considering. Tweedle Dee and Tweedle Dum are spin offs of Tetch, Ratcatcher most people wouldn't even recognise as a Batman villain. Dr Destiny is out as well, although again he's not really a Batman villain, and Catman would just make people laugh i think.
So that being said, i think Riddler will be the main villain and the second one will either be Penguin or Black Mask, or, because apparently it's sacrilege to make a comic book movie without putting in a fuckin' love interest, Catwoman will probably appear in some form or another, even if it's just Selina Kyle.