The one thing the Nolan movies have done extremely well, in terms of creating a deep mythological feel to them, is to focus on Batman's relationship to Gotham - that is, it's been Gotham at stake in each of the two movies before. Ra's wanted to destroy Gotham to cleanse civilization. The Joker wanted to break Gotham's spirit by sowing chaos. Bruce has wanted to fundamentally change Gotham so that he could feel he had corrected his own tragedy, and therefore, go on to live a normal life. At the end of The Dark Knight he's plainly given up on the idea of living a normal life, by taking Harvey Dent's sins onto his own head - and with Rachel gone, his main motivation for desiring a normal life is dead.
Each of the previous movies has also had Batman triiumphing (saving Gotham) but at great personal cost - In Batman Begins his family home destroyed, his beloved mentor revealed as a betrayer and madman, his love alienated; in The Dark Knight, his love dead, his hopes for being a redeeming symbol to Gotham twisted as he is now believed to be a murderer - basically he has nothing left.
So Dark Knight Rises is likely to start with a much more hard-bitten Bruce Wayne - a man without hope, only a grim determination to fight on and on, believing somehow that by fighting he's still making a difference. But this determination by this time probably seems more like madness, especially if Gotham has descended further. Or if it decends further in this story due to Bane's appearance, which seems to be the direction it's been hinted that the story will go.
If the ending didn't sit well with Warners - well, I've always felt the voice over at the end of TDK felt a little tacked on, a way to try to snatch a triumphant ending out of the jaws of a pretty dark close. I would expect something similar here. Nolan's Batman rarely wins - he mostly just manages to barely hold back chaos from taking over. I wouldn't be surprised if this movie ends with an embittered, rage-filled Batman who has truly become something frightening. Nolan seems to be telling the tale of an idealistic young man who makes an extreme choice to dance with darkness, and slowly gets taken over by it, losing love, losing hope, being hammered into a hero who is inches away from the things he fights. Rather than Batman dying or being maimed at the end of this movie, I imagine we'll see him snap Bane's spine, or some other equally vicious tactic that begs the question of what has Bruce become in his effort to save Gotham - a hero or a monster?
That's a theme that many of the Batman comics have embraced, but I could see where a studio would want a more uplifting ending for a tentpole summer blockbuster.
