Here's what I'd like to see:
OSWALD COBBLEPLOT is a Bruce Wayne type. Billionaire. Owns his own company (Penguin Pharmaceuticals or some such nonsense). Short and pudgy (philip seymour hoffman) but incredibly charismatic and a big competitor of Wayne Enterprises. He also uses the company as cover for ARMS DEALING, and has basically sold weapons to every criminal element in Gotham.
GOTHAM CITY streets are becoming a warzone, with criminal gangs outfitted with machines guns and bazookas, children are even being gunned down on their way to school.
The Batman? Isn't around as much because the police are constantly hunting him. In fact, CITIZENS begin to start calling for the BATMAN, putting them at odds with the police. There are CITIZEN PROTESTS in SUPPORT of BATMAN, which end up with a riot against over-zealous cops who are friends of the dead cops from TDK, and Gordon has to wonder if he should go to Batman for help even with his own dept chasing Batman.
When LUCIUS FOX refuses to sell Wayne Enterprises to Penguin Company, Oswald hires a brilliant hacker-digital-anarchist type to try to infiltrate Wayne Enterprises and find something to use... while in there, this hacker, who has a flair for the dramatic, likes leaving little riddles as calling cards when he breaks in somewhere, gets access to EVERYTHING, and finds a connection between Wayne Enterprises and BATMAN (by seeing the schematics that the accountant in TDK saw, as well as other equipment).
Gordon finally has enough when a schoolbus of kids is blown up, and he calls off the manhunt and calls in Batman to help. This results in his own department hating him and he gets FIRED! But Batman is out there helping.
Oswald thinks Wayne Enterprises is "funding" the Batman. He uses the schematics his hacker found to create special weapons designed to infiltrate the Batmobile, Bat-armor, and everything else and starts selling THAT STUFF, making a ton of money because gangs want stuff that can stop the Batman.
Meanwhile, this hacker guy, who leaves riddles on the sites and systems he infiltrates, has a ? as his calling card, is more of an anarchist, and while hacking into Wayne Enterprises, finds the remnants of the SONAR MACHINE from TDK. Meanwhile, Penguin, hoping to eliminate any evidence of what he's been doing, orders his thugs to gun down "? Hacker guy".
"? Hacker Guy" barely survives, and decides to go after everyone with a vengeance. He uses the SONAR MACHINE to learn secrets, sell locations of people, spy on people and blackmail, and then hacks into all of Gotham's security systems, shutting EVERYTHING DOWN and holding the city hostage for billions.
Gotham is plunged into a no-computer dark age (imagine what happened in Die Hard 4, except, it doesn't suck like that movie did). Like at the end of the Dark knight Returns, you remember, when Batman had to restore order? Batman goes to take down the hacker (who as you all must have guessed is basically The Riddler re-imagined), however, at the last second, Penguin's Thugs gun down the Riddler, making the situation semi-permanent.
This is the big climax, the city goes nuts, criminals with horrible weapons, cops trying to keep order, mob rule, kids in the crossfire, think "No Man's Land" crossed with the "nuclear winter Gotham" of "The Dark Knight Returns", Cobbleplot declares him and his companies the owners of Gotham and uses gangs outfitted with his advanced weaponry as his army.
Batman has to swoop into the city and restore order. He sweeps through, taking down armies of villains, eluding cops, saving citizens, enlishing the Bat-vigilantes to follow his way and learn how to be real heroes, fighting his way all the way up to Cobbleplot, and taking him down.
By saving the city during his darkest hour, he regains the trust of the city. Cops still want him, but the people believe in him. Batman, Gotham's true Protector!