Thanks to the OP for posting a very interesting theme.
My take is that one must always be aware of context. And the context in which this series was originally developed was that of the end-game of a 50-year old, worldwide Cold War between political/economic communism and democracy/capitalism. There's a Real Life reason for why Roddenbury had this ship (and its TOS forbear) named "Enterprise," after all.
The total collapse of commuism, the euphoria which accompanied it and the imagined hopeful consequences that might flow were all reflected in the scripts of the early years of ST:TNG. At the time in RL, many otherwise level-headed political philosophers were seriously writing in terms of the "end of history" and for more than a brief moment, it actually appeared possible that the idealistic appeal (as opposed to the harsh reality) of the United Nations might indeed set the way forward as to govern the conduct and relations between sovereign nations.
All this seeped in to some degree into ST:TNG in the first year and we should have probably seen a gradual change of emphasis starting to permeate the show sometime in season two, if not for the writers' strike, which pretty much ruined the rest of that season as a result.
What is most obvious about season 3m in retrospect, and which is absolutely confirmed by BOBW I (which first aired in June 1990), is not so much that the scripts improved (as they certainly did) as a direct consequence of the end of the writers' strike, but that the episodes (with exceptions) took on a darker, more nuanced mood, much more in keeping (almost reflective) with the increasing uncertainties and concerns playing out in the RL.
ST is an ideal. So is the Prime Directive, which is why we see Picard break it every now and again. Yet, the maxim that seems to infuse ST:TNG all the way through its 7 seasons is that "the ends don't justify the means." It sets forth a clear moral position very early on and Roddenbury's death nothwithstanding, pretty much remains true to this philosophy (which of course, Roddenbury would have known originated with the Greeks, yet may have left him somewhat ambivalent by the knowledge that they only suvrived into the modern era as a direct result of the writings and influence of the Catholic Church, and St. Thomas Aquinus in particular.
I take some comfort from the fact that the ST:TNG characters (in the scripted scenarios they were given to play with) tried to uphold that maxim, and I think that maxim is a universal. So it will always have something to say, even to viewers with a post 9/11, Iraq and Afghanistan wars, perspective.