I don't know who Jonathan Hickman is, and damned if I could be arsed looking up his Wikipedia entry, but I'm calling his "S.H.I.E.L.D. was an arm of H.Y.D.R.A." plot as a swipe of the ages-old "U.N.C.L.E. was an arm of T.H.R.U.S.H." fan-fic theory.
I don't know who Jonathan Hickman is, and damned if I could be arsed looking up his Wikipedia entry, but I'm calling his "S.H.I.E.L.D. was an arm of H.Y.D.R.A." plot as a swipe of the ages-old "U.N.C.L.E. was an arm of T.H.R.U.S.H." fan-fic theory.