Happily, my theory holds a bit of weight, what with there already being a line of comics entitled "Iron Man: Director of S.H.I.E.L.D."
Any fan of Marvel's comics can tell you that just because it's been written doesn't mean it will make it to the big screen. There are multitudes of different story lines and character backgrounds for each and every Marvel character that it wouldn't make sense for most to show up in the established MCU. However I do think that the movies, most recently "Civil War," may be alluding to Tony Stark taking over for Jeffery Mace in the near future.
S.H.I.E.L.D. must return to the MCU eventually...
Right? I can't imagine Coulson and friends would sit out the upcoming Infinity War, unless they get an episode of "Agents of S.H.I.E.L.D." dedicated to their side of the fight. It just doesn't make sense for S.H.I.E.L.D. to stay in the dark during a big event like that. With that being said, should the Avengers rejoin forces with the organization that brought them together, a big name actor with stakes already firmly planted in the MCU would only make sense in the place of director. Samuel L. Jackson had his run as director, and though he still has 2 more appearances remaining on his contract as Nick Fury, I'm sure it'll only be to kick some ass or give the team a pep talk, like he did in "Age of Ultron." Nothing against Jason O'Mara, but Marvel Execs clearly like keeping their TV and film properties separate.
Tony Stark is the core of the MCU.
Mostly because of Robert Downey Jr.'s star power, but also because he's a fantastic character. He is constantly tested and pushed to his limit, and he is the stem of most issues plaguing the people of the MCU. While he and Cap quite literally split up the leadership role while they were both Avengers, Tony has been left with the team and even has a web-slinging protegé by his side. We'll get to see Iron Man in action again soon in the upcoming "Spider-Man: Homecoming," and then again in Avengers: Infinity War and presumably the movie that follows. I greatly expect Steve Rogers to be killed soon, leaving room for Bucky or Sam Wilson to take over as Captain America, but also possibly to remind Tony that none of them are invincible. Even though that's his reason for developing Ultron, I think seeing Cap die might make Tony Stark stop and think about his future. It seems as though he's becoming a father figure to Peter Parker and may possibly want to ensure that he's always there for him, by stepping out of the armor and passing Iron Man onto someone else. Then he'd be available to oversee the Avengers and S.H.I.E.L.D. if the story panned out that way.
This would make for quite a cool turn of events in the MCU, but at this point it's just wishful thinking. It would be an easy way for RDJ to keep the paychecks rolling in if he wanted and it would certainly make sense in the grand scope of the series.