My guess is that we will learn that the reason Fury brought Coulson back to life, assigned him this detail with the plane/crew, was because Fury was already...
Winter Soldier Spoilers.
...suspicious of HYDRA's infiltration of SHIELD. He knew that the ONLY people within SHIELD he could trust 100% was Coulson and May, and letting them build a team from the ground up was a way of making a contingency plan for when **** goes south. May is reporting on Coulson's (and the team) status directly to Fury via the encrypted hardline. The show will continue to be called "Agents of SHIELD", because they are truly all that is left of SHIELD. Fury will work remotely with Coulson's team and use the team to root out HYDRA operatives where he can, until he feels the time is right to come back "on the grid".
I could be completely wrong on that speculation, but if not, I think AoS is really going to be a fun ride the rest of this season and next, if renewed.