If there's one thing I know about Sam Jackson, it's that he doesn't fuck around. He signed a contract with Marvel to make something like 28 movies, he let his frustration with Martin Landau beating him at the Oscars be known immediately, and when he asks you what's in your wallet, you'd better damn sure say Capital One, or he will end you right then and there. Therefore, when Sam Jackson says that S.H.I.E.L.D. will come back to the MCU, you'd better believe him.
As we all know, the events of Captain America: The Winter Soldier revealed that the organization had been corrupted many years ago by Hydra, but in a new interview with Coming Soon, Jackson said that S.H.I.E.L.D. will return. When asked if there was still a place in the MCU for S.H.I.E.L.D., Jackson replied thusly...
Yeah! For sure, definitely. Why wouldn’t there be? There’s some way of fixing what they created, and hopefully somebody has that going on or Nick Fury is out there — wherever he is, probably hanging out with Jules and walking the world — figuring out what happened and how it got to that particular place. Maybe they’ll find out that all that was part of a ruse to get to something else also. That would be great. They’ll bring me back somehow, some way, for some reason. I mean, they didn’t have me around to referee the kids when they didn’t go to their rooms and got in this big old fight. We’ll see what happens.
Jackson basically told us what we all already knew... Without Sam Jackson around, shit goes south in a hurry. The writers knew it was smarter to just leave him out of Civil War altogether, because he would've put a stop to that shit long before people were trading blows at the airport. So when Sam Jackson says that Nick Fury and S.H.I.E.L.D. will be back, believe him, because he doesn't fuck around.