I could see the Riddler as sort of a more extreme version of the Zodiac killer. Batman's detective skills in bringing him down might be what gets him back somewhat on Gotham's good side.
Sometimes, I feel like Ra's al-Ghul just has to come back. I feel like there's a 2nd chapter to his relationship with Batman that we haven't seen yet. (And I'd like to see more Scarecrow just because Cillian Murphy is cool. 8) )