I wouldn't want them to begin the sequel too long after TDK. Maybe six months. Maybe a year. At most.
Since Nolan loves Long Halloween/Dark Victory, I'd love for him to bring in Janice Porter as the new DA. That'd be a great nod to the comics.
And I'd really love for Nolan to delve into the mixing of mob and freak. He showed us the mob using freaks to their own ends, but the freaks ending up destroying the mob. And that was awesome. Now they should show us the mixing. Penguin and Black Mask fit this role perfectly. They're at war with each other over who gets Gotham.
Bob Hoskins as Penguin and Guy Pearce as Black Mask. Hoskins is perfect for Penguin. He's only 5'6, and looks a lot like Penguin from the comics. Compared to Philip Seymour Hoffman who is 5'9.5". Guy Pearce is perfect for Black Mask in that he can be and does look like the anti-Bruce Wayne. Good looking, rich, but emotionally and morally bankrupt. Companies struggle and hemorrhage money, he can play a really good, classy kind of bad guy and is a great actor. And since he isn't that great a businessman(he was given everything he has, never earned it), his companies could fail and Wayne could bail them out, furthering his hatred for Bruce Wayne and pushing him further into his Black Mask persona.
Which could greatly mirror Bruce's own troubles. Batman being hunted by the cops even more viciously than before, no one publicly on his side. Pushing Bruce more and more into his "Bruce" persona. But, Bruce being Bruce, he feels guilty over what's going on. He tries to make up for it by building the Thomas and Martha Wayne Foundation. I think that'd be a really cool dynamic for this movie.
And since this isn't the Batman 3 story ideas thread, I'll stop there.