Yeah, The Riddler should really be darker and far more interesting a character, he'd be interesting to see used in the Nolan Verse. He should be something like a cross between the BTK and Zodiac Killers, both known for puzzling the cops with their MO the BTK killer in particular known for calling and taunting the police.
I imagine a Nolanverse Riddler as more of an organized crime kingpin who runs the rackets like a chess game. I mean, that fits the MO of Nolan's Bat-villains; Ra's and the Joker were both master manipulators with multiple layers of mindfrakkery to be peeled back before you got to the core of their plans, and if Bane is anything like his comics counterpart (rather than the disappointing screen adaptations to date), he should be much the same.
And his rival crime boss could easily be a short guy named Cobblepot who fancies himself a member of high society and has been known to commit assassinations with a dagger concealed in an umbrella...