If I rebooted the series. I'd go with Hugo Strange and Red Hood for the first movie (obviously setting up the Joker). I've always liked Hugo Strange, and he was among Batman's first villains, but I feel like in the Nolanverse he would be a little to much like Scarecrow now since they re-invented Crane's image a bit.
Although Gotham Knights already covered Deadshot I'd still like to see him get live-action treatment as a Batman villain. He's a bit flashier than most of the random hitmen and thugs, but his costume is such that it kind of already fits in Nolan's re-imagining of Batman. I mean essentially he's wearing a variation of the Bat-costumes we've seen, but with guns.
Black Mask is another villain I feel works well. Good character, intriguing appearance, kind of is a mobster like you had in the first movie, but escalated. Certainly opens up a lot of story possibilities, and has personal connections to both Catwoman and Batman himself.
Finally...*sigh*...The Riddler and Penguin. I *sigh* because you can't NOT use them, but I feel as though I've seen too much of them.
I have a huge soft spot for Killer Croc and BANE, and honestly, I'd love to see a Knightfall-esque movie, I'm not just sure how the audience would react to having Batman incapacitated for an extended period of time in a movie.