Captain America: Civil War - I'm still riding high, so this one is subject to change. At the moment I think its better than Winter Soldier because, despite some logical leaps like the villain's plan, the conflict and characters were very enjoyable. Having some of the best action in the genre doesn't hurt. I even like Zemo. I like an MCU movie villain who isn't Loki, that's crazy.
Captain America: The Winter Soldier - This raised the bar for the series in a big way, with a spy movie plot and top notch action.
The Avengers - Mostly because I'm still amazed it happened, partially because I'm still amazed it's good. It wisely made what the audience was thinking, "How can this possibly work?" a plot point in the movie, as the real conflict is whether or not these characters will put their egos aside for the greater good. Most action beats are in some way informed by character and the dialogue the was great. Conspiracy theory: Phase 2 relied too much on comedy because of the praise given to the snappy dialogue in this movie.
Avengers: Age of Ultron - Ultron was a let down, Quicksilver was wasted, and Thor's subplot was confusing. But did you see everything else? More great character interactions, lots more team fighting, more character development, Hawkeye becoming a character, Vision being great with minimal screen time, the opening being the best part of the last movie... If it weren't for the frustratingly inconsistent villain, I'd put it over the first.
Guardians of the Galaxy - Unlikely heroes, classic pop soundtrack, general James Gunnery. All stuff I love in movies.
Iron Man - Pretty much the basic superhero movie in structure, but with such a great protagonist.
Iron Man 3 - Tie with 6. I'm glad the Mandarin wasn't really in it. In fact I love that he wasn't. Anyway, this movie had lots of creative action that I really liked.
Ant-Man - They made me like Ant-Man.
Captain America - They made me like Captain America.
Thor - Not much special about it, but I really like Thor so it's really enjoyable in spite of its flaws.
The Incredible Hulk - The Fugitive but with the Hulk. Same as Cap and Thor 1, I like it in spite of major flaws.
Thor: The Dark World - I like the action and most characters in this more than in Thor 1, but the weak villain and external conflict make me pick the first one over it every time.
Iron Man 2 - A few cool scenes in a largely forgettable movie. Sam Rockwell steals the show as he always does, which is nice.