For example, the way they had Bruce Wayne go from being gimpy with a cane at the beginning then almost instantly back to normal seriously undercuts Bane's beatdown and his broken back later in the film. If they were going to blow up Gotham with a nuke anyway, why did they bother to occupy the city for five months? What was the effect on the people of Gotham? Not that I didn't understand any of these points, but all of them should have been made into a bigger deal than they were.
As for characters: Bane, badass as he is, just wasn't as interesting as Joker or Ras because it's not made too clear what his motivations are for most of the film. It would've been nice to see more backstory or build up for him. Matter of fact, I feel similarly about most of the new characters as well - too much were introduced at once, and there simply wasn't enough interaction with them to make me care beyond superficialities. The Talia Al Ghul reveal is a prominent result of this - despite being a fairly clever and logical plot twist, it felt really weak and underwhelming due to her character up to that point being essentially those adjectives. So much so, that apparently I've forgotten what her character's name was. Hell, even the stock detective character of Foley (Matthew "Pvt. Joker" Modine) was given more depth than either of the main antagonists.
Also, the sentence in general heavily implies that the pacing of the film is all over the place. I did explicitly mention that elsewhere, but in a twist of meta-irony, it's something that I should have emphasised more and made clearer.