I'd have to go with Guardians of the Galaxy. While I fully acknowledge its tonal problems, as well as the possibility that Captain America 2 might be objectively better, Guardians just hits all the right notes for me. It's funny, offbeat, well paced, and still capable of grabbing for the heart when it needs to. It features a great cast who are all decently fleshed out for the time given to them, and I love how cartoonishly, joyfully evil Ronan is. Visually, I'd call it the best Marvel movie by far. Every frame is alive with energy and a distinct visual personality, and the way it repeats motifs throughout (like the outstretched hand or the "ravager spaceship as angel" symbolism) is smart, if presented a little heavy-handedly by the end. It's just great.
The Winter Soldier is my other favorite. Somehow it manages to make its metal-armed assassin, winged jetpack, and flying automated aircraft carriers believable, presenting a surprisingly dark movie that isn't without a bit of well-placed levity. The action is all fantastically shot, the entirety of the movie is perfectly paced, and Robert Redford would have made the Marvel Cinematic Universe's best villain yet if not for Loki. It also did a great job of presenting what Captain America really should be, something the first movie lacked: an image of our country's ideals, trying to accept progress without compromising what he believes in. I really don't have any complaints.