Tobar said:

The rise of Hydra in Winter Soldier brought Tony back into the field to fill the void left by the fall of SHIELD. Similarly, in between the search for Bucky (which is referenced in AoU) Cap has been joining the other Avengers to bust Hydra strongholds.

Phase two continued the setup that started in Phase one for the ultimate showdown in Phase three with Thanos.

I understand this. I'm just still feeling let down by what "Iron Man 3" turned out to be. A wasted opportunity, and a film that does not seem to be necessary viewing like all the others are. If you left "Iron Man 3" out, the only continuity issue there seems to be is the operation to remove Tony's chest reactor. Thor 2, Cap 2, and GotG seem to have much more to do with the coming Thanos arc.