I wrote this idea on Superherohype a few months back. I've made a few changes to it though. So heres my take.
The Joker and Two-Face pretty much left the criminal underworld in shambles in TDK, Roman Sionis who was once the head of major cosmetics company Janis Cosmetics untill it nearly went bankrupt because of improper testing of a new beauty product which left several people disfigured is forced to resign as head of his own company and is bought out by Wayne Enterprises. After this his fiancee Selina Kyle who unknown to him is at the time is a thrill seeking jewel thief known as the Catburgler leaves him. Selena and Bruce start to develop a relationship which drives Sionis mad and he vows revenge against Wayne, Wayne Corp, and Selina. He then creates a black skull mask and uses what's left of his money and rounds up whats left of the criminal underworld who are in a gang war and unites them and becomes the leader of all the major crime syndicates and gangs and begins his reign of terror targeting high ranking employees of Wayne Enterprises and people close to Bruce and Selina Kyle including perhaps Alfred and/or Lucius and Selina's sister. Batman rescues Alfred and/or Lucius but fails to rescue Selina's sister who is murdered. Selina is now decides to hunt down Black Mask and his gang and becomes Catwoman.
While Batman is trying to fight the mob led by Black Mask as well as being hunted by police and as Bruce Wayne is in the public eye because his employees are being kidnapped by BLM's gang, enter Edward Nashton a brilliant yet narcessistic FBI profiler sent in to help with the investigation on capturing Batman. But as Batman continuisly outsmarts Nashton's traps, it slowly begins to drive him psychotic and he eventually becomes The Riddler who is so hell bent on discovering Batmans' true idenity he strats using deadly traps and begins kidnapping and killing prominant Gotham citizens to get Batman's attention. As the Riddler, Nashton sends riddles to the press giving them a 7 day deadline to figure out the puzzle or he will kill a new victim. With still no luck on capturing Batman, the Riddler decides to break his pattern and kidnapps Commissioner Gordon who he belives is helping Batman avoid capture and gives Batman three days to find him before he's killed so Batman must track him down. And to make matters worse Batman now has to contend with Catwoman who has become a vigilante who slowly becomes more violent. While Batman tries to bring these villians to justice, he also finds himself attracted to Catwoman even though she is a criminal.
I think this could perhaps be an interesting idea. The reason I like these villians is after Batman revealed himself to Gotham, I like to think that it made way for the "freaks" to come out of hiding like Joker and it would show just how bad it's gotten since the Jokers arrival. The Riddler being a law enforcement agent would show that you now have freaks working with the law, Black Mask would show that the mob is now under the control of a freak and Batman falling for Catwoman whould show that Batman himself is falling for a freak. Also as most know both Batman Begins and TDK had underlying themes. In BB it was fear and in TDK it was escalation and likely the theme for the third movie will be redemtion therefor I would like to see more focous on Batman like in BB. One idea that I also had was because of the pressure of being hunted by the law and outcast by society not to mention the death of Rachel and Harvey (if he is indeed dead) still haunting him, I imagine Bats/Bruce is in a very dark place in his life. I would like to perhaps see Batman really loose control and nearly kill someone. Realizing he is starting to loose it he decides to seek redemtion not only in the public eye but in his own as well, and finally except his role as Batman.