it's not even that The Riddler is one of the few remaining well-known Batman villains, it's that he's one of the few that would be easy to translate into the Nolanverse. Mr. Freeze, Poison Ivy, The Penguin, Killer Crock, The Ventriloquist, and Clayface aren't going to be showing up any time soon. And Ras al'Ghul wasn't even that well known to the general non-comic-reading public. Catwoman is easy in a sense that she can be portrayed as a female version of Batman, one to take up his mantel of responsibility since the public believes he went back on his morals; but really she has her own agenda against the mob (go read Batman: Dark Victory, which I believe the next film should draw heavily from).
To be honest, I'm quite surprised the Riddler is in this. He was always my favourite villain, but I really thought Nolan would explore paths with less-known or under-used villains.
The Riddler is not confirmed as the villain in "Batman 3" as of yet. People are just speculating that Nolan will go with him because he's one of the only remaining 'top tier' Batman villains (along with Catwoman and Penguin, the latter of whom Nolan has gone on record saying he has no interest bringing back to the big screen) and his pathos and MO make sense in the gritty, down to earth Nolanverse.


I mean come on!