Came across this article, and it's a very interesting take on how Star Trek has changed with the times, and how modern audiences seem to have a harder time trusting institutions or imagining Trek's utopia.
And even this is the central conflict of many TNG episodes - it's a little more indirect, but the eternal question of "how do we navigate the Prime Directive" is essentially a conflict between the characters and Starfleet (it's their rule, after all).