S.H.I.E.L.D. are an essential part of the Civil War storyline and, given that they currently no longer exist in the Marvel Cinematic Universe - having been revealed as being deeply infiltrated by HYDRA for years - they absolutely must be re-established before a movie about the arc can be considered. Not only did S.H.I.E.L.D. assume the brunt of enforcing the Superhuman Registration Act under acting director Maria Hill in the comic book arc, they also gave superheroes the option of working for them once they signed up for it, which would enable them to earn a salary and benefits like those earned by other American civil servants. Plus, in the event that an entire group of people opt against signing up for the act - such as Atlanteans or the Inhumans - S.H.I.E.L.D. could even the odds in the final battle by supplying agents to fight on the pro-registration side.