While it made for an interesting story, and if you choose not to look too deep in to it you can just enjoy the ride, the long-term parasitic infiltration of S.H.I.E.L.D. by HYDRA, which was revealed in Captain America: The Winter Soldier and subsequently explored in Agents of S.H.I.E.L.D., really doesn't make much sense. It certainly seems as though the decision to allow this to occur wasn't something Marvel had in mind when the Marvel Cinematic Universe was first established. Why, for example, would S.H.I.E.L.D. have actively recruited the Avengers if their highest-ranked agents were HYDRA operatives? Why would they have allowed for the resurrection of Phil Coulson? Why did they continue to recruit genuine heroic agents like Fitz and Simmons? So much of what they did prior to the big HYDRA reveal just doesn't compute.
