I really wish they'd used The Riddler for the Dark Knight Rises, Bane was actually an excellent choice of villain and if the telling wasn't great, the perfect story elements were there, but the Riddler is fantastic.
Doesn't the Riddler have a really good arc too though that you didn't mention? I read on TV Tropes that one time the Arkham people work on his complusion and cure him of it but it just means now he commits crimes without leaving clues, but eventually he decides to become a detective and earn respect that way etc...
In any case, the Riddler and Joker are perfect villains together, they are both wacky but one in an intelligent way and the other in a manic one.
Chris is right Batman has an excellent gallery of villains because they each take a different aspect and have their own slot and most of all, they all say something about Batman. The Riddler is Batman's intelligence and the Joker his moral standing. Raz is Batmans sense of duty, Bane is Batman's competence and willingness to see a task through. Scarecrow is his use of fear and Penguin... I'm not sure about Penguin but Penguin is cool.
And then add in some Catwoman, Harley Quinn, Poison Ivy.(although why are all his female villains hyper sexual? I love Harley Quinn's origins enough to forgive it though and Catwoman in TDKR was brilliant)
As for Two-Face, I dislike Two-Face in 'duality' mode, the Dark Knights take, of a lawyer who becomes convinced that the only form of justice is random chance, is very cool, but someone obsessed with the number two is not so much)