Spoilers of course.
Just like the Lord of the Rings films, the three in Nolan's Batman trilogy get progressively worse until it's hard not to wonder whether the first one was really that good or it just got the benefit of the doubt because it wasn't a complete botch. In Nolan's case he definitely focused more on the more ill-considered aspects of the first film, perhaps reading his own press too much. All the good parts of the first two films basically came out of The Long Halloween but left without the structure he mostly picked and weakened from there Nolan for this film was left to his own devices.
It's hard to argue that The Dark Knight Rises should be 164 minutes especially considering that it's not at all a complex or involved story - bad guys steal a bomb, good guy doesn't think he can take care of business. Trim all the brooding and elaborate discussions of things nobody should need to talk about ("We need The Batman!" "No, no we don't." "Yes! We do!") and about an hour of useless material would be gone. Nolan, though, is nothing if not a ponderous filmmaker. My guess is that he believes he's telling a Hero's Journey but he follows the Lit 101 conception so closely that there's hardly any point.
To have needed years of work, the script is remarkably sloppy. Its most clever twist is the apparent change to Ras al-Ghul's child - Bane? Nope, it's Talia after all though it's obvious that we won't be getting a Damian in future films. I was never quite sure what prompted Bruce's vision of Ras that revealed some of this. We get one person who figures out Bruce Wayne is Batman simply by looking at him but another trained in observation and critical thinking who doesn't realize this until the end. (Actually I thought the film was making a point that everybody knew considering how often this is discussed - did none of the thugs who heard Bane say this not talk with anybody else?) There's a nuclear explosion right offshore that apparently has no negative effects. Alfred sends some unknown hired help to take dinner to Bruce's quarters (well actually an entire wing but still). Who on earth would send their entire police force underground? Why was Bruce sent to The Pit instead of simply being killed? (Which I think may have been explained but am not quite sure.) Why did nobody in The Pit mention that The Child was a girl? The big conflict at the end is pretty tension-free considering that it starts with lots of activity in one day and then everything pauses for five months, clearly so that Batman can find some way to escape The Pit and make his way back from wherever that is located. This almost seems to be two scripts mashed together which may also explain the length - after cutting large parts of both nobody realized much more still needed to go. (And I can't help wonder if the name of the potential new Robin was deliberate - James/Jim Blake vs Tim Drake.)
Other parts of the script are pure Hollywood default thinking (the very implausible bomb timer), done for visual reasons (police making a frontal assault on an entrenched position when there are clear options), unnecessary characterization in the mistaken belief that's what serious storytellers do and so forth. Sure much of this is true of some quite good films but those were either entertaining (which TDKR almost never is) or were in some way grappling with whatever art grapples with (which TDKR completely fails to do). It doesn't help that motivations are often fairly opaque and not in a nice way. So Talia and Bane want to destroy Gotham to complete her father's mission? Which is what? Urban renewal? Are we supposed to think they're insane or that there's some actual reason? And on the other end Bruce Wayne's fiancee dies and he goes on an eight-year pout? Yeah ok this is actually some form of depression but somebody that out of shape and damaged just can't jump back into the game. (And while it's cool to see Thomas Lennon in a high-profile film he seems out of place as a doctor.) What we get of course is Batman saying that really "Batman" is supposed to be an inspiration for anybody, anybody at all, but what are shown is that only billionaires with cool toys can do this.
Which makes me wonder if the digs on the Occupy movement were deliberate. No matter how much was in the original script clearly Nolan & co had to decide to leave much of this in, leaving TDKR as Romney's most expensive campaign ad. The conservative slant of Frank Miller's The Dark Knight Returns has often been noted but Miller created a complex, resonant story while Nolan's borders on propaganda. The only good news is that he's done with this though an executive producer credit on the upcoming Superman film doesn't bode well.