The Dark Knight Rises wins this one for me.
I won't be using spoiler tags since you should have seen the movie anyways to even vote, so yah...
I enjoyed the acting in Iron Man 3, but that was the case for the past two IM films as well. The story? Lacked terribly. The whole idea of Killian wanting Stark's help was left without an answer(how can Stark perfect it? All of a sudden he knows everything about Extremis when we know nothing of this except for a brush off one-liner to Pepper) or even the reason why Killian did all of these things to begin with(as well as it being a total inconsistency to the Ten Rings' portrayal in the first film). The Mandarin was a joke when Ben Kingsley could have gone down in history as portraying a very scary villain, but instead he ended up becoming more like his character in The Wackness than anything else. Aldrich Killian, a character already in the comics, being the real Mandarin is a complete slap in the face to all the fanboys that wanted to see a great version of Mandarin, not for two villains to be one. If I wanted that, I can just watch Ivan Vanko in IM2.
With Bane, even though it seems as though he's thrown aside once Talia makes her reveal, Bane WAS a threat in the first place that broke Batman and he was the physical foe Batman had to get through as his other foes he dealt with mentally and spiritually/emotionally (Ra's al Ghul, The Joker).
Pepper having Extremis...ehhh....I suppose she could have helped out in The Avengers 2, lol, but I didn't care for the idea. I DO, however, am intrigued on the supposed deleted scene of Killian seducing Pepper and having a sex tape that he shows to Stark for leverage(if that makes any sense, lol). If you don't believe me, it's on CBM.com where Black and Pearce talk about deleted scenes.
I really liked that Harley kid though. It sort of goes back to Stark and Yinsen from the first film. That's one example of how the acting wins in this film when all else fails.
Also, I mentioned this in another thread, but when some feels that Gotham City's voice and soul should've been felt the most in TDKR, I find that S.H.I.E.L.D. needed to be used the most in this film. A supposed terrorist is involved and nothing from a branch of the government that's meant to deal with terrorism. Hell, at least use Hawkeye since we haven't heard a peep about him showing up in Thor: TDW, Captain America: TWS or GOTG.
Iron Man 3 has more problems that I can't wrap my head around. Call it being biased, but I expected more from IM3 while my expectations were meant with TDKR.