My thoughts on what should be in Batman 3:
At the end of the Dark Knight, Batman is on the run, and taking the blame for the 5 people Harvey killed. So, he has to prove to the city (or the cops, at least) that he is a force for good and didn't kill anyone. That has to be resolved, and if Harvey shows up at all, I think it should only be in flashbacks to what really happened.
Bruce really did seem to be placing any hope of a normal life/relationship on Rachel. Now that she's dead, he has to deal with that. Does he go down a darker path, realizing there is no good way out? What does he think of the prospect that there is no end in sight? Is being Batman for the rest of his life a good thing, or a curse?
I think this could be a good way to get Catwoman in. Bruce/Batman is intrigued by Selina/Catwoman, and he probably feels a bit lonely as his one true love/one of the few people he trusts with his secret Rachel is gone now. However, when Bruce finds out that Selina is Catwoman, he realizes it can't work. Catwoman, I think is the most logical villain, and also the most popular one that hasn't been done yet by Nolan. (but please, do not cast Angelina Jolie. She's too obvious.)
As for other possibilities and villains, Deadshot could be good (though he might make people think of Wanted). Possibly Hush, but the whole point of Hush was that you thought it could be one of the other villains in disguise, so I'm not sure how you'd do that at this point in time. Same with the Holiday Killer, maybe. I think they could pull off bringing back Ra's Al Ghul if they really wanted, but I doubt it. The Ventriloquist would be interesting, but I've always wondered why his henchmen take the puppet seriously. I never really liked the Riddler. I love Harley, but she needs the Joker. Based on Ra's comments in Batman Begins, I don't think Talia Al Ghul is a serious possibility.
The Mad Hatter would be really creepy in the Nolan-verse. I'd suggest the storyline where he kidnaps a bunch of runaway kids, including Barbara Gordon, and makes them have a tea party with Babs as Alice. (Of course, I'm a huge Batgirl fan, so I just want her to show up. Forget Robin.)