While Marvel movies have managed to keep in PG-13 so far, recent news reveals that The Avengers, the first ensemble title in Phase 1, was originally rated R for a scene that was later edited to be less graphic. If you haven't seen the film (please go do so, and) stop scrolling now to avoid SPOILERS:
"Well, whenever you impale somebody from their back and the blade comes out their chest, there are issues."
Recently, Movies.com sat down with Marvel head Kevin Feige, who revealed that Phil Coulson's death scene was originally much more graphic: Coulson is impaled on Loki's blade, and it's shown in full "bloody" glory.
"When we submitted [The Avengers](movie:9040), the first couple cuts of it came back from the MPAA rated R. That happened twice," said Feige. "So we went back and had to make adjustments."
The comparatively more realistic violence of [Captain America: The Winter Soldier](movie:254973) seemed to really outweigh that of The Avengers until you think of this scene. Not to say that Loki's overall mass genocide was in any way nonviolent, but when it comes to personal scenes like that particular "farewell" in The Avengers, hitting hard with violence against cherished characters brings the audience to the very dark realization that Superheroes, even in fictional worlds like this one, can't save everyone.
(Until, of course, you start watching Agents of S.H.I.E.L.D. and you remember that this is comics: nobody ever stays dead.)
That leads somewhat into [The Avengers: Age Of Ultron](movie:293035) if what the actors have to say turns out to be correct: the team is now completely without S.H.I.E.L.D. and only have one another to rely on, but a new problem and hints of the team 'breaking up' before reforming under Cap's watch with Scarlet Witch, Quicksilver and Vision throwing in. With the outright horror of Ultron's power (Seriously, the Ultron bots look scary as heck) will the next Avengers film have to go through the same revisions as it's predecessor?