Batman Begins was pretty much Year One.
The Dark Knight was pretty much The Long Halloween.
So...I'd place my bets and say that the third movie will pretty much be like Dark Victory; so that would add more sense to having Riddler and possibly Catwoman.
But if I was Nolan, I'd do the complete opposite and make the third movie more like War Games(but with some significance of Dark Victory, such as the addition of DA Janice Porter):
Have Black Mask raise awareness with the gangs and trying to unite them because Joker pretty much destroyed the gangs apart from the duration of The Dark Knight, so BM is trying to unite them all into one mega-gang while also trying to compete against Wayne Industries as Roman Sionis using his own company(have it called Sionis Tech maybe...it would further explain on the bounty hunter idea and where the weapons and tech comes from). He then decides to use his fame as Sionis and also help the police in tracking Batman down, so he seems like a great man with a great corporation behind him, he's helping the police in their manhunt against Batman, but he's also becoming a crime lord as Black Mask.
He then gets the police into letting him bring in some bounty hunters(See what I meant!), two specifically known as Deadshot and Bane(there could be other ones, but obviously lesser-known than those two) and an all-out war begins with the bounty hunters against Batman. Batman finds his way out of that mess and slowly comes to the conclusion that Sionis is Black Mask and defeats him(I'm pretty certain that the third film's main villain will kill themselves, as it fits the pattern of die, live, die).
And during that process, I want some build-up of two other things: Gordon once again becomes the solo good-cop during all of this and again helps Batman while trying to bring in other good cops from other districts to fight against the corrupt GCPD. And also in the movie, there is a new district attorney named Janice Porter(someone who was very close to Dent during college as well), who from the very beginning, does not think Batman is the villain that Gotham City has portrayed him to be and she even contacts Batman to let him know that she believes his innocence(a backstory involving Harvey Dent's sporadic episodes could be told via Porter(that's why she doesn't believe Batman killed Dent) so we further understand why he became such an evil person THAT fast during TDK).
The end of the movie sees Batman realizing how much he needs to be Bruce Wayne but also how much he needs to be Batman and decides to spend time as both equally, and so starts to date, and his first date is Janice Porter(I'd rather not bring in Selina Kyle if another female can be used, ala Porter). The date goes along fine until he hears sirens and then excuses himself and gives Porter some money for a taxi as he runs off and the film and trilogy ends off with Batman atop a building, peering down as the new Bat logo shines up into the sky.
Main villain - Roman Sionis, AKA Black Mask
Minor villains - Deadshot, Bane, and others such as a psychotic arsonist named Firefly, or maybe even a Joker-esque wannabe by the name of Mad Hatter(who aren't given first and last names, just their 'villain names')
New characters - District Attorney Janice Porter, Detective Harvey Bullock(another corrupt cop as Flass was in Batman Begins)
Cameos - Dr. Thomas Elliot(after another scuffle between Batman and Scarecrow(yes, Scarecrow needs to return for one more time) Batman returns Crane back to Arkham and hands him off to Dr. Elliot(you see his nametag, as he wouldn't need to have a lot of lines)), The Iceberg Lounge(a regular place that Roman Sionis attends)
<----Penguin
