Here's a basic proposal.
The Riddler, in disguise as a honest do-good civil attorny or activist blames Wayne corporation for heavily polluting the nearby water sources. (Of course, this is really the Riddler's work). Wayne obviously knows he is being hustled but the Edward Nygma is such a seemingly honest man that Wayne doesn't associate him with the crime.
Trying to clear his own name, Bruce Wayne brazenly puts the Batman alter ego at risk. Of course, Gotham is still weary of the Bat since the events leading to Dent's death and something goes wrong where it looks more like a cover up by Batman and now both Bruce Wayne and Batman are now public enemies #1 and 1A in Gotham.
To fix the situation, Bruce Wayne must use not only brawn but also guile and investigative skills (finally bringing to the big screen the DETECTIVE label the Batman character earned over the years in comics and cartoons).
Thats pretty much all I got. Add another baddie to either add sexual tension (Catwoman) or fight scenes (Bane, Clay Face, Killer Croc, etc). Finally wrap up the ending where Batman and Bruce both earn redemption in Gotham.