Well, if Nolan doesn't have any ideas, here's a few from me!
The third movie should continue Bruce Wayne's struggle with what the Batman persona means for him. I would bring it to a resolution by giving serious consideration to ending the third (or 4th) movie with Bruce stepping away from being Batman. Either due to injury, the personal costs being too high... or because he has a successor. If Year One
was the inspiration for Begins
, why not have Bruce Wayne's involvement with Batman come to an end like in The Dark Knight Returns
As for villains, I would make them the corrupt city and police. One of my criticisms of Nolan's Batman movies is that Gotham is too clean, not corrupt-looking enough. Sure people say
the city is corrupt, has no hope, but it doesn't look
it. For the next movie, turn Gotham into a true urban hellhole. In the third movie, corrupt city officials, like the mayor, or other business elites, want to take over the city and run it the way they think it should be run; i.e., the Golden Rule: those who have the Gold, make the Rules! Part of this plan is to continue making Batman the scapegoat, justifying creating a police state in Gotham.
Having the City be the enemy doesn't mean no cool costumed villains. I would use The Riddler and Bane: Eddie Nygma is an eccentric, crazed genius, who the fatcats bring in to help run the investigation against Batman. Bane is a no-nonsense enforcer, who beats up, tortures or kills anyone (crooks, cops, civilians) they need info from, or gets in the way.
As Bruce struggles against the forces of officialdom, he has to deal with the personal fallout from the end of DKR. Maybe bring in Catwoman or Talia for a love interest. Have Bruce become a detective and spy as he uses his billionaire status to infiltrate the cabal. Meanwhile, Riddler and Bane are closing in on him. If they want to do a fourth movie, you could have Bane break Bruce's back a la Knightfall
, and set up the fourth movie being about training Bruce's replacement: not Robin, or Nightwing, but another 'Batman', a la Batman Beyond
To complicate things, you could have Riddler actually working for two sides: the remnants of the mob as well as the other billionaires. Or he could even be reporting to a mysterious figure who is only revealed at the end as Ra's al Gul!
The point is, if I could come up with some non-sucky ideas, surely Nolan can. Bring us Batman 3!