At the end of the _Agents of S.H.I.E.L.D. _Season 3 finale, the show fast forwarded six months after Hive's defeat and Lincoln Campbell's death. By this point, Phil Coulson was back in the field, and he made a passing comment to Mack about S.H.I.E.L.D.'s new director. So now we know that Coulson isn't in charge anymore, and while the identity of this new director hasn't been disclosed yet, actor Clark Gregg knows which character he wants to lead S.H.I.E.L.D.: Melinda May.
While discussing some of the hanging plot points in the Season 3 finale, Gregg told EW that if it was up to him, May (played by Ming-Na Wen) would be S.H.I.E.L.D.'s new director in Season 4, and Coulson would be completely on board with that. As he put it:
I'd love it if it was [her]. That would be magnificent. She has earned that right and she is a commander that Coulson would absolutely follow with absolute loyalty.
Melinda May has been part of Agents of S.H.I.E.L.D. since it premiered in September 2013. She and Coulson already had years of history with each other before the series kicked off, but in the pilot, he recruited her to join his new S.H.I.E.L.D. team (though we later learned she was also asked by Nick Fury to keep an eye on Coulson). Since then, not only has May proved to be an asset in combat, but she's also bee valuable for her keen bullshit detector, whether it's calling out Coulson on some of his questionable decisions or other members of the team for their behavior. Not that she doesn't have her own flaws or moments of vulnerability, but she's certainly proved how capable she is enough times. She's served as a good second-in-command before, so her becoming director would be a welcome promotion.
Unfortunately for Clark Gregg and other May fans, the chances of her taking the lead might not be as strong as assumed. Gregg also addressed how Captain America: Civil War's ending seemed to indicate that S.H.I.E.L.D. would be "turned over to autonomous management." In other words, an outside party from elsewhere may take the reins rather than someone already in S.H.I.E.L.D. Someone that comes to mind right away is General Glenn Talbot. Obviously he's an experienced military man, but we've seen time and time that his interests and strategies usually don't match up with S.H.I.E.L.D.'s. Whether it's him or someone else, be they a new character or someone established, it's a safe bet that eventually the status quo will shift back to normal, and Phil Coulson will be back leading the spy organization sometime during the next season.
Agents of S.H.I.E.L.D. Season 4 will premiere on ABC sometime this fall.