So many thoughts about this movie... First of all, I really liked it while I was watching it, but less than an hour after leaving the theatre was ripping it to shreds.
Like most of Nolan's films it works better on an emotional level than a logical one. There are tons of plot holes... but at the time of viewing they didn't really bother me. Most movies have a plot hole somewhere in them, and I don't think it's always a big deal. For this movie... It's pretty sloppy because there are just so many of them, but at the same time the characters are pretty solid and that makes up for a lot of it, unless you're the type to just nitpick movies to death while watching.
My big major, no excuse problem of the film is that the villains have no real motivation. Spoilers and whatnot. So Bane is part of the League of Shadows and ostensibly his goal is to continue the work of Ra'as al Ghul. My question is: WHY? Ra'as wanted to destroy Gotham because it was a city "beyond saving". But... Batman SAVED it. It's been 8 years since The Dark Knight and the crime rate has dropped dramatically. Organized crime is completely gone. Gotham is no longer a diseased arm that must be cut off for the good of the body. Of course... there's the really obvious twist concerning Ra'as's daughter, Talia. Turns out she's actually the main villain... But the motivation doesn't change. It's still, ostensibly, continuing her father's work. Well, that, and revenge. Revenge is, in my opinion, generally pretty weak motivation. Especially when the stakes get raised as high as they do in this movie. The actions of the villains don't seem justified by their own logic.
So that was my beef with the film (while watching it). I kept waiting for the twist about why the bad guys were actually doing all of this... But it never comes. I also feel like the backtracked on the whole theme of the trilogy. If you look at them, they're less about Batman's character and more about the state of Gotham itself. Joker calls it a battle for Gotham's soul. I really like that about the movies. So... why didn't they save the Joker story for last? The first movie works fine. It's about Wayne becoming Batman and choosing to save the city. But the second movie... This is where it should have been a movie about Batman's actual struggle to save Gotham. Technically The Dark Knight does this, but my problem with it is that the villain, Joker, is set up as a destroyer of the pure and doesn't actually represent the "evil" of Gotham. Another bad guy (there are so many good ones to choose from) would have fit the theme better. Then, the last of the trilogy... Joker. Batman has seemingly saved the city, but here comes Joker to say, "What, you think these are good people? I'll show you they're not."
That's just my take on it... I'm sure people don't see it that way or think it's stupid but whatever.
Quite frankly, I agree with the last part of what you said Mitsu, like a lot. However, this is my theory: I have a feeling the last movie was not intended to be Bane and whanot. Seeing as how Heath Ledger died...they probably had to rework the third? I don't know.