After the epicness of TDK, i'd like to see a smaller, more focused story. A detective story. Bring the story back to Batman instead of the city wide focus of the story in TDK. An intriging, complelling mystery for Batman to solve, something the cops can't solve and Gordon, behined his teams back, is forced to ask Batman to be involved in, even though Batman seperated himself from the police at the end of TDK.
I wanna see the character of Batman evolve - even at the end of TDK, i still think we're in the 'Batman Begins' era of Batman lore, i.e - his quest is still only just starting, and the Batman we know from the comics still isn't fully formed on screen, both mentally, physically and astheticlly. Somewhere in the third film, i wanna see the character fully realised - the suit, the car, the cave, the tech, the mission.
I wanna see more Batman moments, something that was sorely lacking from TDK. Stealth, suprise, even goddamn batarangs. Get him in the shadows, get the grapple gun out more - little things like that.
And i'd really love if the voice was toned a little. I watched BB for the first time in ages the other day and voice is so much more subtle than the the one used in TDK.
Better fight choeography, direrction and editing.
Everything else, i'd leave to the Nolans. They seem to know what there doing.