It's never too early for Batman III speculation. Hell, I've been speculating about it for at least the last year. Now that The Dark Knight is in theaters and stealing money faster than the Joker strung out on ten cans of Red Bull, I can start slinging my unfounded theories about the next film—which I hope will be called The Dark Knight Returns, even if it doesn't directly relate to the Frank Miller graphic novel of the same name. Specifically, I'm going speculate wildly about possible villains, 'cuz that's where the fun is.
Everything I am about to say here comes from my own diseased brain, and not from any substantial rumors. At this point, nothing about the third movie is certain; it's all rumor. I know that Goyer and the Nolans have some ideas, but I can't read their minds and they certainly aren't saying anything at this point. If I could read their minds, I'd be the next Bat-villain.
Running through the rogues gallery, here are my musings on the possibilities of them appearing in Batman III and what might be done with them. First, the villains who have already appeared (and there will be some big spoilers here about TDK:
The Joker: No. Not happening. Dealing with Heath Ledger's legacy isn't something any filmmaker would want to tackle. Leave the Joker alone.
Two-Face: Is Harvey Dent dead? The ending of The Dark Knight leaves the issue ambiguous, with Jett at Batman-on-Film certain that Two-Face has landed tails-up permanently, but most everyone else believing that the ambiguity denotes that he's still alive. Two-Face's legacy must be dealt with, however, regardless of whether he survived. It seems that the character's arc is complete, so he wouldn't need to physically return, but I would like to see him again, and the Brothers Nolan and Goyer could find more for him to do. It's no longer necessary however.
Scarecrow: Let's have him appear in every Batman movie!
Ra's al-Ghul: Another ambiguous death. Is Ra's al-Ghul immortal? Are his methods supernatural? The League of Shadows is too large and multifarious to go down after one failure, and it would be simple to return them to manipulating the tragedies of Gotham city. I even wondered during The Dark Knight if Ra's was actually behind the Joker's madness. The Joker is the sort of villain that Ra's al-Ghul would think Gotham deserved.
Onto the newcomers:
The Penguin: Please! I want me some Penguin! He's one of my favorite characters! Done as a stylish English gangster, he could work. I hear people calling for Bob Hoskins, but my pick is either Philip Seymour Hoffman or Andy Serkis. Please, Christopher Nolan, give me the Penguin! You can make him work! "Quack, quack, quack..."
The Riddler: The buzz among most Batman bloggers is that the Riddler is the #1 choice. Many have postulated that the character of Coleman Reese in The Dark Knight is a set-up for the Riddler, but I don't see this happening. However, the Riddler would make an excellent follow-up for the Joker, and he would adapt easily to the new setting. My pick for the actor is Guy Pearce, who has previously worked with Nolan in Memento.
Catwoman: Another hot rumor. Batman's love-interest file is now wide open, so I think Catwoman has a good shot. The feminine appeal would be a great hook for a next film, makes for great billboard material, and would sit well with another villain. She wouldn't be too much of a stretch in the realistic Nolan-verse. But... there is that Halle Barre thing, that black stain on all DC films. Can Catwoman be rehabilitated? Does Warner Bros. even want to risk it?
The Ventriloquist and Scarface: Here's a villain who strikes a balance between silliness and possibility. I can envision an insane but meek man using a ventriloquist dummy as his outlet for his violence and criminal brilliance. On screen, would this just end up hilarious? The animated Bat series both used versions of the Ventriloquist effectively, on live action is a different affair.
Mister Freeze: Fans have screamed for a while for Patrick Stewart to play Victor Frieze. His tragic nature and his superb rendering on Batman: The Animated Series make his one of the strongest characters for the new franchise. The problem? He's too science-fiction for the realistic Nolan-verse. Could the filmmakers overcome this? As with the Penguin, I'd love them to try. Stewart is the right choice, by the way.
Bane: Of all the villains to appear in the earlier Burton-Schumacher films, Bane got the worst deal. He needs rehabilitation, and he will fit well with the gritty setting. Make him a criminal schemer hopped up on super-steroids with an obsession about beating the bat. A semi-adaptation of Knightfall would make a killer film, although perhaps this should be the fourth movie instead of the third.
Killer Croc: I would normally say that Killer Croc was too outrageous for the realistic Nolan-verse, but the anime film Batman: Gotham Knight managed to make a believable version. Since he's had a semi-official introduction into current continuity, tied into Scarecrow, I think he might make a good supporting, plug-ugly villain combined with someone like Penguin or Riddler. Mad Hatter could slap K-Croc with a mind-control device, and away we go.
Harley Quinn: Too closely connected to the Joker. Pass.
Black Mask: This villain, who has a skull mask permanently attached to his head, is perhaps the easiest fit into Christopher Nolan's Gotham city, since he's essentially a psychotic gangster. He isn't well-known among the general public, but Bat-fans often mention him as strong possibility. The Nolans and Goyer could fit him into Batman III without even breaking a sweat. My only hesitancy is that he's the most obscure with laymen among the main contenders for head villain.
Poison Ivy: No. Just... no.
Mad Hatter: Bit too colorful, although his violent psychosis would adapt to this Batman's world. The mind-control angle would make it easy to bring in some thuggish villains.
Man-Bat and Clayface: Great characters. But too fantastical. Trying to make them more mundane would end up ruining their appeal.
Firefly: A lesser character, but a cinch for the realistic setting. As a supporting villain, I think this pyromaniacal nut would ideally suit any situation.
The Clock King: I'm getting obscure now, but I love what Batman: The Animated Series did with him, and it wouldn't be hard to put him into the Nolan-verse. It won't happen, but someone has to kick it out there, and I shall be that one.