It hit me suddenly today while I was reading a Batman comic. I proceeded to write my thoughts down and I wanted to get some feedback on this, so I came here. Now, I have this (what i believe to be) great idea of how the Riddler could work in the next Batman movie. He isn't a 'Joker-lite" character or side villain like the comics portray him. His intellect alone could make him just as great a foe for Batman as the Joker, Penguin, or Black Mask ever are. He uses his intellect for his own personal gain and not to help the general public.
Now his character in Batman 3 could work like this. Imagine the police having trouble trying to crack down Batman and figure out his identity. They find clues but it only leads them to dead ends. They hire a man who is known for his high intellect, his love of puzzles and his great detective skills. Enter Edward Nigma.He's been hired by the police to figure out Batman's identity so the police can capture him. What they don't know is his background is filled with various criminal activities and an OCD related mental problem involving puzzles. He could be declared legally insane. So by now the police have told Mr. Nigma of the Joker and the damage he caused to Gotham City. Nigma figures out quickly what Joker did wrong with trying to unveil Batman and Nigma quickly develops his own modus operandi. Nigma stays working for the police for about a month before his grand scheme can come into place. Nigma at this point pretty much has the police under his control by ordering them around and figuring who Batman could possibly be. The police now have two new threats along with Batman coming straight at them. One of them is a man who robbed a bank and left no trace except for a riddle and a new mob leader. They ask Mr. Nigma to handle all three of these cases and he realizes this falls in with his master plan. Enter Black Mask. Black Mask leads a double life as a new head of the mob and head of a big business corporation that is being ran into the ground by Bruce Wayne's company. Knowing that he could go broke, he turns to illegal weapons dealers so the mob can get rid of Bruce Wayne. Batman is getting in their way so Black Mask has to kill him too. Edward Nigma understands Black Mask's problems and sends an invitation to Black Mask for a secret conference.
Going under the guise of the Riddler, he proposes an idea to Black Mask. Have Black Mask work for him and have the mob do his dirty work and he will provide Mask with funding to get his corporation started again and he will let him have Bruce Wayne. Realizing this isn't an offer he can't pass up, Black Mask excepts. The Riddler now has the police and the mob under his control. He can keep misleading the police and he can keep using the mob to get closer to Batman. He pulls off a murder and leaves a riddle for Batman, telling him that the city is in danger id he doesn't reveal himself to the public. Now Batman has a new threat and the police and mob on his tail. After more crimes, he quickly figures out what the Riddler is doing here. He decides to let some mob members go after fighting them and he secretly tails them. They meet up with the Riddler at his base of operations and Batman comes in confronting the Riddler. However, the Riddler knew Batman would tail them so he set Batman up. He reveals two assassins, Deadshot and Bane. Batman attempts to fight them off but Bane proves too strong and captures Batman and in the process, breaks his arm. Deadshot fires a tranquilizer dart at Batman and he ends up in a coma. Batman is shown tied up and being questioned/lectured by the Riddler. He tells Batman his plans to put Gotham City under control and he tells him that he's already got 2/4's of the job done. He goes up to Batman and asks him "what am i going to do next?". Batman answers i don't know and then the Riddler unmasks him, revealing Bruce Wayne. Now he can terrorize Batman on a deeper level that no other villain or criminal in the past could. He decides to let Batman go, satisfied with cracking his identity and yet he decides not to tell the police. Instead he waits a few days before breaking some of his captured mob men out of Arkham Asylum. He carefully orchestrates a break-in and frees some of his more dangerous mob servants. They go to Bruce Wayne's mansion when he is out as Batman and they kidnap Alfred. They also find out of his connection to Lucius Fox and kidnap him too. The Riddler commits a quick robbery and leaves another riddle for Batman about their kidnappings. He realizes what's happened and he goes to rescue them.
Outside of the Riddler's building are some guards. Batman easily defeats them and he quickly figures out the layout of the building and where Alfred and Lucius and the Riddler would most likely be. he quickly goes through the building and reaches the top where Riddler has set up an ambush. Batman defeats the gang members but more come at him. Riddler quickly interrupts and tells him that these two will die slowly and painfully if you don't stand still and let my crew beat you to death. So he willingly gives in and is starting to get kicked and punched. He sits there taking the damage, able to do nothing. Riddler even gets a few hits in himself. However, Black Mask enters the room and holds a gun to the Riddler's head. Riddler nervously asks him what he's doing, he screams and then gets a bullet shot in his head. Black Mask now tells everyone to stand back and he goes to shoot Batman when Batman gets up and starts beating the crap out of him. Black Mask fights back, but Batman tells Black Mask that he warned Gordon of this and he comes in through the window with a S.W.A.T. helicopter and goes in and rescues Alfred and Lucius. Black Mask is also captured by some police and is sent to Arkham.
The movie ends with a public announcement of Batman renouncing his title so long as they don't press charges against him. He unveils himself on television as Bruce Wayne and tells them that Batman is no more, that he did his job already and hopes people are inspired to fight injustice too. He then leaves, escorted by the police, not under arrest and finally free to be himself again. He tells Alfred a joke, he laughs, and they head back to Wayne Manor.
Now this is just a basic idea. I haven't got full plot details but tell me what you think of it and please offer criticism and feedback. I really enjoyed writing this.