Amanda Waller is the DC universe's preferred government agent. She's best known as the leader of the Suicide Squad, a team of villains who are promised amnesty in exchange for serving on a government strike force, but she's also worked with Checkmate, a more traditional spy organization, and had a position in the government when Lex Luthor was President. She's bright, very clever, a strong leader, and wields the power of the federal government.
The main reason I see her as a potential foe for Batman in a follow-up to The Dark Knight is that Batman is cast as a dangerous outlaw at the conclusion of the film. In the animated Justice League Unlimited, Amanda Waller headed up the government's response to a perceived superhero threat, and the season-spanning arc detailing Project Cadmus's efforts under Waller to deal with the Justice League situation is one of the better superhero stories I know.
Pros: If the Feds get involved with the Batman problem in Gotham, Waller would be the perfect choice to lead them.
Cons: Detours to Asia in each of the first two movies aside, the movies are all about Gotham City, and bringing Washington into the picture, in the form of federal agents, might detract from that a little. Also, with every comic book series seemingly headed for the big screen these days, Warner Bros. might want to save Ms. Waller for a Suicide Squad movie.
How I'd do it: Waller and a group of soldiers show up at Jim Gordon's office, telling him that Gotham City police aren't equipped to handle a criminal like Batman, he's too well-equipped and he's already shown (as far as everyone but Batman and Gordon are concerned) that he doesn't mind killing cops.
Casting Guesses:CCH Pounder voiced the animated Amanda Waller, and since she looks the part as well, I have a tough time imagining anyone else.
Verdict: With no supernatural abilities and an easy entrance into the story, I'd say she's an excellent fit. Really, if there's federal involvement in the hunt for Batman in "Batman 3," for lack of a better title, I'd be disappointed if we didn't see at least a cameo Amanda Waller.
After The Scarecrow, Ra's Al Ghul, The Joker, and Two-Face, who should be Batman's next enemy in the Batman Begins/The Dark Knight series? Well, as of now we know that Tom Hardy will play Bane and Anne Hathaway will play Catwoman.
Check out the master list for all the villains covered. I've pretty much run out by now. Obviously, there are more Batman villains, but not any of significance that I know of. As of February 2009, no one is confirmed as a villain. Not the Johnny Depp Riddler, not Phillip Seymour Hoffman Penguin, nobody.