Johnny Depp would be my foremost choice. He definitely has the eccentricity needed to pull him off, though I'm not quite sure if he could blend it with the element of realism the first two movies had.
And anyways, it's not that the Riddler is better or worse than the Joker - the two characters are apples and oranges. The Joker tends to be there to test Batman's will while the Riddler's there to test his intellect.
Ra's al Ghul can kind of play both fields, so I'd also like to see him return at some point. (He's probably my favorite villain from the comics.) Plus, his "The Reason You Suck" speech in Batman Begins was just epic.
Getting back on topic, though, probably Depp as the Riddler - and there's a LOT of potential for him as a character there. I don't think the films have fully realized Batman being a detective. And having the Riddler there would probably be as good a chance for that as there's ever gonna be.