Fact that Thor, Incredible Hulk and Iron Man 2 took place at same time we learned from Fury's Big Week comic books. I don't think events at Phase 2 took place in real time movies came out. What if we get Fury's Big Week vol 2 or something and it'll tell us real times everything happend.
I'm suggesting this because I think Iron Man 3 was chronologicaly last movie in Phase 2. What if Iron Man 3 takes place at christmas 2013 and not 2012 and for this time, SHIELD was already down. I say what if Captain America: The Winter Soldier happend before Iron Man 3 and that's the reason SHIELD didn't take a place in IM3