No offense to Mr. Duchovny, but Start Trek under Abrams is profoundly "uncool"; it's popular, yes, but I'd hope Mr. Duchovny, who has expressed confusion over the popularity of Star Wars, recognizes Abrams' work as very much an homage to that more than the more political Star Trek.
Star Trek: Deep Space Nine (1993-1999), especially from Season 3 onward under the control of Ira Steven Behr, was the most politically insightful and dramatically realistic (with great moral ambiguity) of all Treks. It had the guts to have a freedom fighter heroine call herself a "terrorist," rather than a "freedom fighter," as a means to challenge American viewers' conceptions of how that word was used by the biased media; indeed, actor Alexander Siddig has even stated that much of that was a metaphor for the treatment of Palestinians. The writers even used the name "Maqius" (named after the French resistance movement against the Nazi-occupied Vichy regime) for those resisting an occupation brought about by the redrawing of boundaries by the United Federation of Planets (the UN or US), but called it a "terrorist" group as well.
So, not only did this fine show explore issues of terrorism as a result of occupation; identity politics (with Odo sympathetically having divided loyalties between the "solids" and his changeling people); religion; and a proper sense that conflict often comes from differing interests and perspectives, rather than an inevitable clash between our "good" heroes and their "evil" opponents; indeed, the Changelings behaved very much like the Israelis or Stalin's USSR in being so defensive as to effectively not care about the fate of those living in the buffer zones they seized. Even Gul Dukat is a wonderful study of the charming and admirable aspects of what can turn out to be some of the world's cruelest and pettiest dictators. His fall was painful for many viewers to watch, but it gave us insight into how difficult it is to spot those who practice "evil" and how they can be good as well.
All this is in stark contrast to the superficial, cynical, "shock and awe"-driven, machismo-laden rubbish contrived by Abrams for purely commercial purposes.
In fact, Deep Space Nine, like The X-Files, foresaw certain historical themes that were forgotten by the mainstream media in the '90s and over which came to the forefront after 9/11. These include the idea that "our" side is capable of violating its highest principles in the name of fear and "the other" is just as capable of kindness and cruelty as we are, though DS9 perhaps drove that theme more thoroughly. I remember remarking in the '90s how preposterous it was for The X-Files to suggest that the military would abuse human rights -- so ignorant I was of US Cold War actions in the Third World -- or even torture Mulder in the finale; a few years later, Abu Graib happened and extraordinary rendition was well-known. The X-Files absorbed the lessons of America's folly from the Cold War and never forgot them, even though the mainstream US media wanted us to.(continued)