I think what I liked about the TNG-era Star Trek was that, as often that there was an "antagonistic relationship with their superiors in Starfleet and/or the civilian leadership of the Federation", they also as often get along. The Federation was a government that worked. That was the baseline assumption. The show demonstrated it, the characters believed it. They were proud of being a part of it, and not just because of some ill-conceived patriotism.

Related to that is the baseline assumption of competence. Characters in Star Trek, especially ones from the Federation, were always assumed to be extremely competent and good at working together; everyone valued excellence. Sure, they were exceptions, but they were that - exceptions, around which a story or a joke could be built. I miss that world of excellence in other shows.