Re. Lapis Exilis:
Those are some really interesting points. I hadn't really looked at the natural growth of Batman, Gotham and its villains in such detail in Nolan's Batman. But you're right, I think, and I agree that it's making the movies better than the competition (I can't really think of any exceptions).
So, just based on the situation at the end of TDK and the points you've made, wouldn't the Riddler be a good choice? The Joker arguably threw all of Gotham into incredible chaos and the only way to resolve that chaos and madness was for Batman to go along with it to a degree by accepting responsibility where he's not responsible at all.
With the chaos and the opening left in the underworld wouldn't the Riddler be a pretty natural development? He would seem similar to the Joker at first as his schemes would not at first be apparent. But it would become clear - at least to a character such as Bruce Wayne / Batman - that there's actually a clever mind with a plan at work. However, this would be plan you could actually figure out in some way.
So, on the outside, the Riddler would continue some of the madness and chaos but, really, it wouldn't be like that at the core.
Wouldn't that be a possible direction to take?