The end of the last one sets up a story rife with "One Last Ride" undertones, IE most of the movie being about Bruce Wayne and him being on an involuntary sabbatical, exploring the possibility of shedding the Batman persona, slowly getting used to fighting social injustice as an influential public figure, slowly getting addicted to this new (yet oh-so-familiar) persona -
'beloved by the people, hated by the wicked'-
-then against the wishes of his inner circle, being forced/compelled/addicted to don the costume one last time.
That being said, I think they're going to bankrupt him and out him. Strip him of his financial clout, deny him his Batman persona, and you arrive at the essence, at the core of what makes him a hero (or not)...
Bruce Wayne, having to keep a low Bat-profile, instead turns to his alter-ego to find avenues to help Gotham. Tying in with you-know-who's "
The day may come when Gotham no longer needs Batman..." speech. Bad guy (Riddler, probably) outs him and suddenly the entire core group of good guys: Gordon, Fox, all removed from power in that single stroke.
Into the vacated void of power pour new figures who seem like genuinely grateful blokes: thanks to Gordon's testimony they pardon Batman (not Bruce Wayne), but not without implying that Batman is never to make an appearance again. We've got everything under control now, thanks very much. They're not necessarily bad guys quite yet, but you can see them growing to like their money and power. Riddler taunts Bruce Wayne over how futile all his efforts really were, how his personal losses were all in vain, how silly his caped-crusader phase was in that light, how his escape into his Bruce Wayne-hood - regardless of his altruism - was just another form of all men's lust for power and adulation.
Then set the law on his Wayne persona. Batman is too respected to be punished, but Bruce Wayne is just a man. Have the government freeze his assets and tacitly allow his competitors at his family's empire and legacy, the citizens of Gotham watching as their Camelot crumbles, helpless to circumvent that which is Institution. He is nationally vilified, his political connections flee from him, and for the first time in a long time he feels truly powerless, trapped, frustrated, with no outlet, with the elusive Riddler serving as mouthpiece for his own confusion and self-doubt. Nothing, not even a man as powerful and well-connected as Bruce Wayne can break the rules mandated by society's aspirations towards civilization.
Is there nothing that can?
Yes, people then realise that the whole playboy thing was not what he was really about. It would also close the storyline that may/may not have begun from the ending of the Dark Knight where Batman is cast as a villain.
Both characters could be redeemed in the events of his heroic death.
Doesn't that sound, well, I don't want to say kiddie, but I wouldn't bet on Nolan going for something like that. That's very "Oh-poor-me-I'm-full-of-teenage-angst-and-no-one-really-understands-who-I-truly-am". They got that out of the way (wisely) in the first movie.
If they do kill him I'd wager it'd be in a way that he looks the villain except to the audience/circle of friends.