Much like TDK, it's a movie where I feel like so much about it is fucking fantastic, yet severely held back by small issues and some really stupid shit that just kind of culminate and linger every time I watch it.
The Batwing thingie chase at the end was bad. Some of the most piss-poor action directing but Nolan has never did an impressive action sequence. He's gotten close a few times, but compared to Spielberg or Cameron he just doesn't seem to have it. The Bane fight at the end is pretty great and to me should have been the action climax and not the chase. I would not say that if the chase were good.
Marion Cotillard... terrible, not even counting her parody death scene. I like her plenty, but her performance and character were just completely awful and shoehorned.
The forced Catwoman romance, yikes (why that kiss amidst a chase scene, Jesus) and actually showing her and Bruce at the cafe at the end is terrible writing. You'd think Nolan, who tries to be a little psychological here and there, would understand that just simply a satisfied look from Alfred would have told us, or would have at least let us guess that Bruce was alive, and that's all we would have needed to know. Instead it's the most ham-fisted CHEERS MOTHERFUCKER bullshit in the entire trilogy. Just way too on the nose where I felt like it could have actually been something a lot more interesting. This is definitely not a flaw depending on the person though, just how I feel about it. I'm not saying it would have left so much more to the imagination, but the way it happens just kind of ruins it for me. I guess... to me it could have just been more tasteful.
Can't think of every little thing, but those are the highlights for me. I have a love/hate relationship with the trilogy. On one hand, so much of it is so damn good. The first 2/3 of TDK is some of the most remarkable filmmaking in one of these things, but even that falls apart pretty bad after Rachel's death (though it starts to recover a bit toward the end). I mostly love the entirety of Begins. TDKR, issues mentioned above notwithstanding, is mostly a pretty good movie. At least Maggie Gyllenhaal wasn't in it, so there's that. Just a very up and down trilogy for me, with some ridiculously insane highs and some unfortunate lows. Still generally good movies and a fun watch.