I saw it resembling the comic book in being confusing.
SPOILERS FOLLOWING for the Sokovia Accords in Civil War (nothing too specific about the rest of the plot).
Civil War made it sound like if you wanted to be an Avenger, you had to register/sign up and that the team would be subject to UN oversight. That was the pitch, you sign the accords to be an Avenger, or you retire. Then things got complicated when Wanda wouldn't sign up, but there was also the question of her not being a US citizen.
But it's still quite a leap from there to the idea that every inhuman or enhanced in the country would have to register, which seemed to be the implication of this most recent Agents of S.H.I.E.L.D. General Mustache was obviously there to see exactly what Inhumans S.H.I.E.L.D. had in the field—a reasonable fit with the Sokovia Accords as explained in the movie, but in other conversations (I think between Skyle and Lincoln, or maybe Coulson mentioned it too?) they made it sound like every Inhuman in the country would have to register. Where's that coming from?
I have no interest in dragging the political arguments from the Civil War thread over here, but you can't ignore that if those were the stakes—mandatory government registration for all enhanced/Inhumans whether they're private citizens or crime-fighting superheroes—that would have to change the way we look at Cap and Iron Man's arguments.
So exactly like the comic book, the conflict seems to be over inconsistently written legislation. Disappointing.