My take on the villains that we don't know will be in a future movie:
Hugo Strange - Could be explained pretty easily, but his M.O. is pretty lame. There are much better villains. Only bring him in if running low.
Catwoman - Definately should be a big part of the series. You can't tell Bruce Wayne's story without Selina Kyle IMO. Catwoman is very easy to explain (similar to Batman, with the suit and whatnot). Would start of as a villain then toe the line like she did in the comics.
Clayface - Maybe, if done like the original Clayface, Basil Karlo. Pretty weak M.O. (IMO) and very similar to other (better) villains. Only use if running low.
Penguin - I disagree with Nolan, I think Penguin is pretty easy to put in these movies. British, called "the Penguin" and has weaponized umbrellas (and if he's a British gangster/arm's dealer that wouldn't be too hard to explain). That's it. As long as you have that, you can do whatever you want with him IMHO.
Riddler - I would rather not see him. Although he could be explained he would come of as a weak, more harmless version of the Joker. Maybe a minor/cameo role.
Mad-Hatter - No. Too silly. Running around trying to get hats on people, bleh.
Deadshot - Maybe, but not very well known. Doesn't really fit the "feel" of these movies, feels more like a Marvel character.
Mr. Freeze - No. Too unrealistic.
Poison Ivy - With her "super powers" over plants, no. But maybe if she's just an insane biochemist who uses her knowledge of plants & chemicals in her crimes, that could work.
Man-Bat - No.
Killer Croc - Hell no.
Black Mask - Yes. Easy to explain. Rumoured he could be in the next movie, which I would like. Hopefully he'll be introduced in a minor role in the next one and become a larger villain in the 3rd (alongside Two-Face).
Ventriloquist - No. Well, maybe in a very small role (like Zsasz in BB) as an escaped inmate from Arkham or something. Who's quickly caught by Batman.
Harley Quinn - I can see her in a latter movie. I think Joker should go to Arkham at the end of TDK or the start of the 3rd movie and stay there 'til like the 5th or 6th (which I think should be the last) movie where he escapes. With minor scenes in the movies inbetween showing him in Arkham, maybe with Dr. Quinzel. But I think she would have to be a much darker character than in the comics/cartoon. Personally, if she's done well I'd like her in, but if she's not I wont be crying.
Bane - No. Stupid.
Hush - Yes. Easily explained and offers something different in that his conflict is personal with Bruce Wayne.
In summary:
Yes: Catwoman, Penguin, Black Mask, Hush
Maybe, if minor/cameo (like Zsasz): Riddler, Deadshot, Ventriloquist
Maybe, if done right: Poison Ivy, Harley Quinn
Only if you have no one else: Hugo Strange, Clayface
No: Mad-Hatter, Mr. Freeze, Man-Bat, Killer Croc, Bane
So that's about 8-10 main/secondary villains (including Ra's, Scarecrow, Falcone, Joker & Two-Face) plus a possible 4 minor villains (including Zsasz) over this new series. Which I think should be about 6 movies altogether. I think that's plenty, and covers the vast majority of the popular villains without breaking the feel of the movies (if done right).
KYG