Avengers Age of Ultron: The pacing is a bit off. I think they needed a slightly longer running time to help smooth out some of the transitions and make it all feel a little less choppy. And they could've at least started by axing Nick Fury's farmhouse speech - that character literally had no good reason to be in that sequence at all.
X-Men 2: Killing off Lady Deathstrike without giving her a single line.
Amazing Spiderman - I don't know exactly why, but Dr. Connors just didn't quite work for me.
Man of Steel: Clark letting his Dad die, even though he refuses to listen basically every other time his dad tells him not to save people and continues to save people even after letting his dad die... Also, I don't care how much you love the family dog, if it's too dumb to get out of the car with everyone else while a tornado is coming, you go to the underpass and mourn it later. You don't run back into a tornado to save a dog. Also - did anyone actually check what those spaceship designs looked like before putting them on film?
Avengers - No earpieces. Also, kind of an easy out with the sudden introduction of the handy dandy override mode.
X-Men DoFP - The happy future is a bit weird. Either it undercuts the drama of everything between 73 and 2020ish, or it will quickly be disregarded or retconned out of existence, in which case, why bother? Also, the magical serum was kind of off - why should a serum designed to repress mutant powers be able to repair spinal damage? And why would the effects just disappear so easily afterwards?
Iron Man - Obadiah Stane
Captain America - Peggy fires a loaded gun indoors at an untested shield because she's jealous.
The Dark Knight Rises - A man with no superpowers can magically heal his broken back in less than 3 months with almost no medical help. Also, an organization dedicated to destroying corrupt places like Gotham City instead helpfully waits 3 months for Batman to heal before actually trying to destroy the city.