I thought I was going to find out when I saw Civil War, but it’s not at all clear.
This balancing act continued throughout season two, when Director Coulson and his new team battled against Hydra, established the Inhumans.
I suspect, in the wake of the Sokovia Accords and the end of Civil War, the people involved in choosing who the director of S.H.I.E.L.D. will be are other than in-house S.H.I.E.L.D. people.
If I know my government bureaucracies, I have a feeling it will be someone somewhat less qualified than Coulson to run S.H.I.E.L.D.”