A couple thigns that bother me:
Did Bruce Wayne fake his X-Ray scans? First off, how could he have THAT much damage to his body, even if it is 8 years later? Secondly, if it was as damaged as they say, he wouldn't have been able to move, and the rest of the movie is ridiculous. I'm going with he faked his scans.
Building on that, I don't think Bane would've beaten him the first time. In the comic, Batman could barely stand and was about to pass out, not to mention Bane was jacked up on Venom, that's how he beat him. Here, Batman was for better or worse at full strength, especially since he would've come back weaker to fight him the second time. (I'll let the magic "Healing his spine" thing go, though there's no way he could be at full strength)
I suppose nukes in the DC universe don't carry radiation, as there's no way Batman could've escaped it from his plane, nor could the city of Gotham. (Though I like the idea of him riding the radiation wave to safety, must have been a lead-lined suit)
Also, Bane really wasn't the villain in it, he was little more than a thug. I figured the whole thing was Talia's plan, and he just executed it, maybe getting some of the little details. (Like reading Gordon's speech on the steps of the courthouse) My biggest problem is that he goes through the whole business of isolating the city and creating an anarchist state with the nuclear bomb...only to have it decay and blow them up anyway. I understand that the normal people didn't realize this until the end, but why even go through that? Why just...I don't know...do it in the first place without all the hassel? There's much less a chance of it being stopped, and it would fit more the secretive nature of an organization called "The League of Shadows." I guess it's just to screw with Batman, like, "Yeah, we did this: All because of you!" It's like their insanity defeats them.
Before it can be filmed, drawn, acted or programed, it must be written.