I've grown up a bit since I last posted on this thread, and I have some new ideas.
The problem with including multiple villains in other superhero movies is thus: The villains only work together out of a mutual hatred of the hero. Think about Sandman and Venom in Spider-Man 3. Think about Catwoman and the Penguin in Batman Returns. Think about Two-Face and the Riddler in Batman Forever. They didn't work. What makes Nolan's franchise so interesting is that the villains fit together. Almost like a puzzle. Warp one villain, and you have to warp every other villain you plan on including. Replace Sandman with Electro, and all that changes is the way a few fight sequences play out. Two-Face could have easily been replaced with the Black Mask, Tony Zucco, or just about any mobster-type villain in Batman Returns with minimal adjustments to the plot. Now, replace Scarecrow with Killer Croc or Nolan's Joker with the Riddler...and the entire movie changes. Having the Scarecrow a key part to Ra's al Ghul's destruction of Gotham; having the Joker a critical component to Harvey Dent's decline into madness...we haven't seen that before in superhero movies. So I'm going to attempt to fit as many villains as I can together in the way Nolan would want it, not the way any other director would.
Here goes:
As much as I love how so many of you have done the Riddler, I have a different idea. My Riddler would be based on the character L from the anime/manga Death Note. To anyone unfamiliar with Death Note, L is the world's greatest detective and aids the police in finding the identity behind the Kira killer. That right there could make for a great Riddler. Instead of having him be some serial killer or whatnot, have him aid Gordon (and maybe even an appearance from Bullock) in capturing Batman. Also, when L is first introduced, he was an unseen character. He only communicated with the police through a laptop. Whenever L spoke to them, the letter "L" in fancy looking calligrophy appeared on the screen. Replace that "L" with "?" and you have a Riddler. For most of the film, leave the Riddler off-screen. Only bring him on near the showdown at the end. A great way to work the Riddler into the other villains would be to simultaneously have him manipulating the cops and other villains in Gotham so that they can all take on the Bat at once.
Another great character to adapt would be Hush. However, don't include the Hush character! How can this be done, you might ask? Simple - just include Tommy Elliot. Have him in Gotham for Rachel's funeral. The biggest change about this Elliot would be his motivation. Instead of greed driving him, make Elliot blame Rachel's death on Batman. Have him HATE Batman the same way Harry Osborn hated Spider-Man in Spider-Man 2. Just don't dress him up. We saw what happened to Harry once that happened in Spider-Man 3...I don't want a repeat of that.
Hugo Strange would be very simple - make him be Crane's replacement as the Director of Arkham Asylum. Ta Dah!
Firefly would also be pretty easy. Have him appear in the first few minutes of the film like Scarecrow in TDK to show how badly crime in Gotham has escalated.
The rest fit together like pieces of a puzzle...
Make Gotham in a state of chaos. Sal Maroni's death left Gotham's underworld with a power vacuum. On one hand, there's Roman Sionis, Maroni's right-hand-man and true successor. On the other is Rupert Thorne, a once small-time crook making the most out of Maroni's death. And there's a mob war between them. Normally, Thorne wouldn't be able to lift a finger against Sionis, but Thorne's men are armed with better weapons. Thorne buys his weapons from a big-time black market dealer known only as the Penguin.
The Penguin, in this film, would run the Iceberg Lounge as a front for his arms deals. The name "The Penguin" isn't a gimmicky name the newspapers give him, but is an alias. The Penguin is to Oswald Cobblepot as The Godfather is to Vito Corleone, Scarface to Al Capone, The Roman to Carmine Falcone, etc.
Sionis, desperate, puts a bounty on Batman's head so he can recruit new and better muscle. One of the people that responds to the bounty would be Lady Shiva. But the bounty idea doesn't work as well as Sionis had hoped, and turns to a recently fired exec from Wayne Enterprises.
Dr. Victor Fries was once the head of Wayne Enterprises' science department, but was fired because he embezzled millions from the company. What Bruce Wayne didn't know was that Fries embezzled all the money to keep his wife alive in a cryogenic sleep. Desperate to keep her alive, he turns to the mob. Roman Sionis offers to fund his wife's cryogenic tank if Fries can build him weapons to compete with Thorne and the Penguin. He develops battle armor and a gun that fires the exact opposite of Napalm. However, Sionis is displeased with Fries' weapons, citing their expense, and cuts his funding. Fries later dons the armor and picks up his gun and attempts to assassinate Sionis.
(By the way, FRIES would be pronounced the same as FREEZE, so there's no reason to include that stupid name)
However, Sionis lives (although is now deformed) and is sent to Arkham Asylum (now under the careful eye of Hugo Strange). In Arkham, he hears tales of a powerful Venezuelan vigilante known only as Bane. After being set free from Arkham (Strange pulls some deal with him - haven't thought that through yet), Sionis dons a black mask to cover his deformities and pays for Bane to be his bodyguard, to protect him from Thorne and now Fries.
And thus, I get my laugh in. Bane originally fills the role of the mindless henchman. However, he gets fed up with it and eventually kills Sionis. Bane reveals his intelligence at this point. This would mainly be a little joke to poke fun at Schumacher's Bane.
That's all I have for now, what do you people think? I've also been thinking of some casting ideas - some unknown Bollywood actress for Shiva, Edward Norton as Tommy Elliot, Laurence Fishburne as Fries. Freeze can be black...?