S.H.I.E.L.D. has been consistently present throughout the MCU - there since day one in the original Iron Man. Even after the organization was torn apart during the events of Captain America: The Winter Soldier, it lives on secretly under the leadership of Phil Coulson (Clark Gregg) who remains loyal to Nick Fury (Samuel L. Jackson).
With this organization seemingly out of the picture during Civil War and Samuel L. Jackson claiming he's not in it at all, the U.S. military has a much larger role. This is where General Ross comes in. This is also where it'd make sense to include a military officer who has a major role to play in the future of the franchise in Carol Danvers, a character you might know better as Ms. Marvel. For a few years now she's been known as Captain Marvel and will be introduced as such in her own 2018 Marvel Studios movie.
Danvers' Marvel Comics origins date back to where she served at an Air Force base as an officer and Security Chief and it'd be smart to establish her in the movies as such before she becomes a super-powered Avenger. How Danvers acquires her super powers can be easily explained by what has been established in the MCU. In the books she's a victim of an accident involving a Kree (introduced in Guardians of the Galaxy) alien device (similar to what was introduced in Agents of S.H.I.E.L.D.?)
All Marvel needs to do know is introduced the original Captain Marvel in 2017 Guardians of the Galaxy Vol. 2 and all the plot elements will be in place for Danvers' own hero journey the following year. Phase 3 could see Danvers go from human officer to Avenger and we'd like to see that story arc begin in Civil War.