The great irony of Agents of S.H.I.E.L.D. is that as the show has progressed and improved, the in-universe justification for a show about S.H.I.E.L.D. has grown more and more tenuous. On the film side of things, Marvel has completely eradicated and discredited S.H.I.E.L.D. – the whole purpose of Captain America: The Winter Soldier, after all, was to show how irreparably broken the institution was from day one. The only solution was to dismantle the entire corrupt system, and yet in Agents of S.H.I.E.L.D. it continues to exist.
The idea of Coulson’s team sticking around to uncover HYDRA cells exposed after the collapse of S.H.I.E.L.D. was a decent justification for a while, but with HYDRA emerging as the main villain every single season, they need a new angle to keep this thing fresh. The Secret Warriors might just be that angle.