Well, if we look at the state of things at the end of TDK...I think the key word is 'disarray'....on all fronts, and the worst it's ever been. Joker's locked up, so what had briefly become a totalitarian underworld crime element, with no more mob bosses left after Joker 'cleaned house', has gotten its head cut off......no order or concept of allegiance whatsoever. The city's beacon of hope/justice is extinguished now that Dent's dead. The new commissioner's trying to put everything on his own shoulders, but now uncovers just how deep the corruption went, and even some of his own task force from the last story were in collusion with the Joker. Then there's Batman...who took enough of a PR hit with the Joker killings, now he's wanted for the murder of the city's martyr...and that's even more strain on Gordon who has to keep the truth from his own people. Basically, things have really gone to sh#t.
So in terms of villains...again, over the last two films, the villains have represented an overall movement/sociological element....not just themselves with their henchmen. With the state of things as described above, it might make most sense if things have degenerated into pure street-justice...pockets of gangs, but relatively disorganized and open war on the streets with no regard to civilian casualties and collateral damage. Might be a good place to incorporate something on the order of the Mutant Gang from Miller's Dark Knight Returns, with Batman realizing that he has to somehow appeal to a group of outlaws by defeating their leader, as opposed to his former philosophy of just punishing them all. Almost a sort of twisted political move by him, since he's now an official outlaw himself. So like in DKR, he defeats the gang leader but almost gets killed in the process...but during Batman's absence (while healing), the gang then affiliates themselves with him like the S.O.B.'s in DKR, becoming a sort of Guardian Angel group who deal out harsh punishment to criminals on the streets. Rather like the 'impostors' in the beginning of TDK, but in larger numbers and instead of Bat-costumes, they have Bat-symbols tattooed on their faces....more tribal, if you will.
Great....just the kind of thing Batman needs...yet more violence amongst the criminals with a bunch of them acting in his name. So again, things get even worse, an S.O.B. is killed by the cops, so the gang storms the police dept and now the city is war zone. There's a blackout, etc.....and Batman finally comes back, like in DKR, and basically declares a state of martial law, getting the S.O.B.'s to do things 'his way', more methodically with the emphasis on restoring a sense of order, rather than just punishment. So that's how Batman 'redeems' his place with Gotham City, I guess. Unfortunately, it doesn't really leave much room for incorporating another one of the traditional 'rogues gallery' villains like Riddler/Penguin/Catwoman/etc., but narratively, I think it could be a good way of upping the scale/stakes that have been established with this particular version of Batman so far.
Just a rough idea of things.
