All things considered, AoU incorporated phase II films as well as it could given what the phase II movies were. Avengers had the benefit of Thor and Captain America directly leading into its plot. No one complains about how Iron Man 1 & 2 or Hulk are nothing more than brief references in Avengers. AoU incorporated the Jarvis' drones, Tony's PTSD, the fall of shield, and Thor's infinity stone romp pretty well. They had major impacts on the plot of the film but the movie wasn't really about any of that, nor did it need to be. Avengers had the benefit of having Cap 1 essentially be a prequel leading directly up to its events.