This is a great thread, I have a lot of these sort of ideas. one that pops into mind right away is Nolan's Batman trilogy. I felt like the third movie really missed the mark on what could have been a great concept. My recipe for fixing it, in much less detail than it exists in my own head:
Dark Knight Rises needs to be split into two movies. You need to build up the stakes, which they were much too rushed on. the first movie is Batman's fall. Bane arrives in Gotham, operating from the shadows and slowly destroys Batman bit by bit--his fortune gone, his technology stolen, his new girlfriend killed, his identity discovered, the police hunting him. In utter suicidal desperation, Batman finally faces Bane. Catwoman betrays him, Bane defeats him and breaks his back. Gotham is now in Bane's hands while Batman languishes in capture, forced to watch it come under martial law.
That is the first movie, it ends on a very sour note. However, during it we meet Catwoman and Blake. Blake is dogging Batman's steps the whole time, demonstrating his ability as a detective. The second movie revolves around Batman finding his way back from total defeat, but also him witnessing that there are others willing to defend Gotham. Catwoman makes a turn from villain to hero, fighting against Bane and his occupation, Blake finds the Batcave and takes up teh mantle of Batman. Inspired, Batman trains himself back to health, returns to fight Bane (and wiser this time, instead of just trying to punch him... again).
Along the way it is revealed to us and Bruce that his girlfriend who Bane killed was actually Talia, and that she is behind this, not really Bane. Bane wants to rule Gotham, to rid of it crime in League of Shadows fashion, but Talia wants revenge. The end involves not just finding a way to beat the unbeatable Bane, but to outsmart Talia. Bruce learns he has to rely on others, not just himself, and Blake and Catwoman help to save the day.