I think having a distrustful government agency was a sign of the times; but it did make for compelling storytelling. It's weird to go back and read old books where SHIELD is helping the heroes, in the back of my head I can't stop thinking of the nefarious stuff they're up to.
I understand that Bendis took Fury off the board before Hickman, but he could have kept him off the board for Hickman - but that's pure speculation on my part.
But they do seem to cooperate on a lot of things. Hickman's Avengers began with Bendis' credo of "Go Bigger"