Overall I like TDKR and think the hate is exaggerated sometimes.
But the middle section with Gotham on lockdown does get pretty clunky and it has kind of an unwieldy narrative structure.
I also have a few problems.
Catwoman and Talia Al Ghul in the same movie limits development for both of them and each's relationship with Bruce/Batman.
Blake should have been better-developed so there's more justification for him replacing Batman at the end, and really Nolan should have just let JGL be Dick Grayson instead of a half-assed kinda sorta not really pseudo-Robin.
Bane mounting this master plan to take over Gotham and then just....hanging out at City Hall for the next five months (?) is kinda lame and also feels like an arbitrary drawn-out deadline to let Batman recover and make his comeback, conveniently just in time to save the day.
I wasn't a big fan of Bane (disappointingly so as I love Tom Hardy).  The voice is just ridiculous sometimes (he sounds cheesy as hell in the Blackgate speech scene), and after taking over Gotham the movie doesn't know what to do with him after that.  He just hangs out the rest of the movie and then gets a throwaway death as a punchline to a one-liner.
Gordon is not as well-utilized as he was in The Dark Knight.  He's just kind of "there", either in the hospital or hiding in JGL's apartment most of the movie and doesn't really do much until the climax.
Michael Caine is actually really good in the few scenes he has, but is also really sidelined and minimized.
That's.....not how repairing a broken back works.
Why exactly is Bane keeping the police alive?
Ben Mendelsohn and Matthew Modine's characters are just cartoonish.