I think the main simple reason why TDKR rubbed some comic fans the wrong way is simply the plot/story Nolan told for TDKR. At the end of Begins you have the Joker set-up/card and it said to fans that The Joker would be in the follow-up. Then at The Dark Knight ending you have Batman on the run from the cops and becoming the villian. But in The Dark Knight Rises it by passes some of those threads and solves some of them off screen to tell an ending to the series. Though the characters are in the state that they are because of the events of the last film. It is a tie-up to everything that has happened in the first two films. -Bruce has done his job but what now... -Batman needs to be the symbol of hope to Gotham he set out to do in Begins, -The LOS makes a last attempt at completing their own mission aswell as getting back at Bruce Wayne. -Bruce lost the woman he wanted to be with now has to find someone else to spend the rest of his life with. -Has to not rely on Batman to live life. -Plus in a new film you also have to introduce some new elements in the new movie. -The Gotham P.D going from corrupt in the first two films to standing up for their city and doing their job correctly with Batman not being needed. But you also have to show that Batman was the right choice for Bruce and his city. Without Batman Gotham would be worse off.