The Riddler's problem in a movie is the same as my impression of most of his comics: he's fun enough, but all he can do is offer a generic Batman case. For a $3 comic, that's okay; for a theatrical film, a generic Batman case is insufficient.
Which is the real challenge if we're playing around with this - not just how the Rogues would fit into the Nolan universe, but how would they fit into a Nolan-verse story? His movies have been quite clever at creating a coherent Gotham City that feels like it works as a real city, and combining several villains far more successfuly than other projects.
With rumors on that Detroit and New Orleans will be sites of the filming of the next movie, sounds like Nolan is going to up the urban decay of Gotham considerably. Perhaps something along the lines of, the citizens of Gotham are demoralized by the murder of their one trustworthy and inspiring public official, dashing DA Harvey Dent, and the revelation that the Batman is a vicious killer, plus the trauma the city went through under the Joker's rampage. The mob is furious at how close they came to going down and, with Lao's and Dent's deaths and the case against them destroyed, are back on the streets with a vengeance. Inspired by the Joker and the general sense of chaos gripping the city, psychopaths who may have been existing quietly in the city for years are suddenly triggered, and disturbing crimes begin to pop up all over the city. The police force is split between corrupt cops making the most of the situation, and good cops under extreme public pressure to bring in the Batman, who is generally blamed for the out of control state of things.
As has been speculated for the next movie, Dr. Hugo Strange emerges on the scene as a brilliant FBI profiler/ criminal psychologist doing the talk show circuit and then asked to consult with the police on the Batman task force and some of the other freakish crimes. Suffering from extreme Narcissistic Personality Disorder he becomes obsessed with manipulating the situation in Gotham to maintain his fame and position as the expert on Gotham's escalating crime problem.
He sometimes secretly frequents the Iceberg Lounge, where the owner, Oswald Cobblepot, is an amusing, charming, corrupt information broker of the underworld. A la Louis Renault from Casablanca, Penguin, as he is called for his tuxes and pear-shaped body, is without loyalty and will cooperate with criminals or the law as he finds useful to enrich himself. He never gets his hands dirty enough to fear prosecution, but does know what muscle to hire when needed - this may be anyone from Dr. Jonathon Crane who still slinks about peddling his insanity-inducing drugs to expert thug Killer Croc (I like the body mod fanatic idea for him - perhaps he has a nearly full-body crocodile tattoo) to the cold-blooded assassin for hire known only as Deadshot. (or these characters could be associated with specific mob gangs - see below)
Penguin's got a lot to trade in these days because after the Lao experience and the death of the heads of two major gangs (Gambol and Sal), the various organized crime groups are no longer observing the spheres of influence they used to respect in Gotham, and an all-out gang war has heated up, leaving the normal citizens under seige. Ostensibly out to solve this problem, Strange instead manipulates information through Penguin to sustain the war, forcing the Batman (his greatest obsession is to discover the Batman's true identity so he can understand his psychology, write a book and retire rich and respected) to be out in force night after night, giving him lots of data from which to work.
That's all I've got for the moment, if anyone else wants to try to weave any of the other Rogues into this. Feel free to modify the above as seems Nolan-ish to you...