I think the pace of the movie is one of the worst things about it. The entire movie goes from scene to scene to scene to scene, until the credits hit. There is no time for any emotion to sink in, etc. The story isn't bad, it's just that there is to much of it. The movie was 2 stories rolled into one, and I felt it hurt the entire vibe, and made it feel "rushed". And since it felt rushed, you barely heard/felt the score in the background, which seemed to take away form a lot of the emotion that was happening on screen.
The characters: I think there are a ton of things about TDK that took away from the spirit of Batman(ie. no lurking in the shadows, Gotham City, hardly any bat-gadgets, wasn't fond of The Jokers interpretation, no cave/mansion etc). If you take away a lot of things that make Batman Batman, then what's the point in making a Bat-flick? Again, TDK is a good movie, but it isn't a good Batman movie, IMO.
The acting: Sure, some actors did better then others, but that's not to say there weren't faults. I thought Bale did a horrible job at playing Batman in TDK, yet, he did a good job in Begins, but his TDK-Batman was a mess. His Bruce Wayne was good, but his Batman? Not to me. I think Maggie didn't play a good Rachel, and while Heath did a good job at acting, it didn't feel like a good interpretation of The Joker, so I guess you can say I didn't like his portrayal. I also thought Micheal J White, who played Gambol, did a HORRIBLE job, along with the SWAT guys and everybody on the ferries.
So again, I think those movies I listed have better overall acting and pace, which leads me to re-watch those movie more then I will TDK.