They've done Man-Bat in a few of the animated series. If done right for the big screen it could be terrifying, but I don't think it could carry a movie as the sole villain --or even work as a nemesis.
They used
Man-Bat three times in the animated series. Each incarnation wasn't that great of a villain. Also, the new line of Batman movies has a more realistic leaning than did ANY other on-screen version of the Batman series. They're trying to root the new Batman in more serious and easier to connect with tones. Cell sonar, kevalar body weave in the suit, malfunctioning gadgets, etc. They gave Scarecrow the ability to truly frigten people with chemicals, not mind-powers, like in the animated series and the comic.
They're taking the athiest's approach to super heroes. No supernatural crap, just real life bad guys that aren't spawned in vats of chemicals or mutate themselves in Jekyll-and-Hyde machinations.
The only thing that they might've done so far that would be considered supernatural is
hint at Ra's Al Ghul's immortality.
This is why I think that if they're going to make another Bale/Batman movie, they'll be using real-to-life psychos.
Here's a list of potential non-supernatural villains:
Catwoman (Only because she's an amazing character that needs to be redeemed from that AWFUL movie with that HORRIBLE actress that I shall not name, who also destroyed the Marvel heroine Storm. I personally enjoyed the rape scene in Monster's Ball because I think she deserves it in real life.)
The Riddler (My absolute favorite Bat villain. If done well enough with the right actor, he could blow Ledger's Joker completely out of the water.)
The Penguin (I really hope not. He's such a limited character.)
Firefly (If used, they could break a record for most explosions in a movie)
Killer Moth (Although, Ledger's Joker pulled the same MO already.)
Ruby Ryder (The ultimate counterpart to Bruce Wayne.)
The Mad Hatter (my second favorite Bat villain after Riddler.)
Tweedledee and Tweedledum (Henchmen for The Mad Hatter would be the ultimate Comic Movie Porn.)
Poison Ivy (could be done well if they don't cartoonize her like they did Uma's version in Batman Forever.)
Catman (He's a colorful character, but extremely limited.)
Deadshot (Could be fun to watch him operate. He's a truly badass killer of Tarantino proportions)
Ventriloquist/Scarface (Only if he's played by Jeff Dunham.)
Villains excluded for their supernatural abilites:
Man-Bat (Mutation beyond the explanation of science)
Clayface (see Man-Bat.)
Bane (Too reminiscient of the Incredible Hulk therefore supernatural, like Man-Bat)
Killer Croc (again, un-believeable mutation = disqualification)
Batzarro (a mutated Bruce Wayne clone is a bit hard to swallow)
Rhino (see Bane)
Mr. Freeze (Mainly because I think the character is simply a ripoff of Iceman from the Marvel X-series. Also a hard-to-believe transformed/mutilated character)
Villains excluded because they've already been used:
Ra's Al Ghul (He is believed to have been killed. Though, not really, he is immortal after all.)
Scarecrow (In Arkham Asylum, but still able to be freed.)
The Joker (Sorry, unless this is Superman or X-Men, you can't use the same villain two times in a row. Ledger's Joker is unique but still replaceable. We might see him reappear in another few films. You have to. He's Batman's #1 enemy.)
Harley Quinn (Can't have her without Joker)
Two Face (Dead)
Falcone (In Arkham Asylum because of an overdose from Scarecrow)
Joe Chill (shot dead)
On another note, does anyone think we'll start to see sidekicks soon? Robin or Dick Grayson was introduced in the third of the Tim Burton movies. Anyone think that the third in the Batman Begins series will reveal the Boy Wonder?
Also, Barbara Gordon was VERY young in the latest movie. It'd be hard to use her as Batgirl for another decade in order to make it believeable.
For those of you ticked about Lucius Fox's knowledge of the Bruce Wayne/Batman identity, he knew about it in the comics.
So, what do I think we'll see in the next Batman movie if they make it? It's incredibly likely that we'll see Riddler or Penguin as the next major villain. Catwoman is a close possibility as well. Robin might not appear, just because I simply don't think that this series is ready for him.
Prospective title that moves along with the current naming trend: Batman: The Caped Crusader or Batman: (insert any other Bat-title).
Alright.... I quit.