According to Agents of S.H.I.E.L.D. star Clark Gregg, the series found its stride when it began to distance itself from the Marvel Cinematic Universe movies. When Agents of S.H.I.E.L.D. launched in 2013, the plan was for Marvel's films and TV shows to be intimately interwoven. Those plans changed in 2015, however, when a corporate restructure split Marvel Studios apart from the wider Marvel Entertainment.
Fans - and, indeed, the stars themselves - have frequently complained at the somewhat artificial division this creates. In theory, everything takes place in the same world, and it's all "connected." In practice, however, those connections only ever work one way. The Marvel Television shows acknowledge the movies, but the movies never acknowledge the TV shows.
In an interview with i09, Agents of S.H.I.E.L.D.'s Clark Gregg has suggested there's a positive side to this division. While he seems to have enjoyed the tie-ins in the first and second seasons, he clearly believes his show is better off standing on its own two feet.
"I think in the early days it was very much an experiment and honestly, Marvel was really one big company, and now it’s really not. I think it’s really two separate divisions and there was a real desire to thread very carefully what we were doing with the movies. You know, at the end of season one with the Hydra reveal in Captain America: Winter Soldier, it turned our show upside down.
But I think when the show started to really find its best stride was when our writers decided “Eh, screw it. We’re going to take what we can get and there’s a lot of stuff [Marvel Studios] doesn’t seem to be using. They don’t seem to be using L.M.D.s, they don’t seem to be using Ghost Rider or the Framework. At first we didn’t believe that we were doing Secret Warriors, but then it became clear—‘Oh, that’s Quake.’ They’ve ingeniously taken the parts of the Marvel universe—which is broad—that no one seemed to be interested in, and we’ve squeezed every drop out of them and really let our train go on its own track."
He's certainly got a point. Beginning with season 2, Agents of S.H.I.E.L.D. began to build its own mythology, introducing the Inhumans and revealing that the hacker Skye was in reality the superhero Quake. By season 3, the S.H.I.E.L.D. team were confronting world-threatening foes like Hive without an Avenger in sight. Season 4 was probably the most creative, though, with Agents of S.H.I.E.L.D. moving to a later timeslot and reinventing itself to embrace everything from supernatural horror to dystopian virtual realities.
There are still loose connections to the main MCU, of course; the threat of Thanos loomed over Agents of S.H.I.E.L.D. season 5. But the series uses those ties as a springboard to launch its own stories; Thanos became the inspiration for a tremendous arc involving time travel and a power enhancer that had the potential to split the entire planet apart like an egg. The plot was steeped in S.H.I.E.L.D.'s own mythology, with only the vaguest links to events in the movies.
To the surprise of viewers, season 5 didn't even feature the snap, and season 6 will air after Avengers: Endgame's release. Given the Avengers are expected to avert or undo the snap, it's likely that Agents of S.H.I.E.L.D. will never tie into the biggest event in the entire history of the MCU. But it sounds as though Gregg thinks that's for the best, and that S.H.I.E.L.D. is better off blazing its own trail.
This raises an interesting question; what comic book elements has Agents of S.H.I.E.L.D. tapped into for season 6? Clark Gregg is keeping quiet. "There’s some strange anomaly happening that feels like a very threatening rupture every time it occurs," he explained to io9, "and there are these people, these humanoid people who show up in the footage and one of them looks a lot like Coulson." There's been some speculation that this "rupture" could be a tear in the fabric of space-time in the aftermath of Avengers: Endgame, a portal through to an alternate dimension, and that Gregg is playing an alternate - evil - Coulson. But fans will have to wait and see whether those theories are correct.
Agents of SHIELD season 6 premieres in May 2019.