[Harry Lime]

They have tried to explain the similarity in the physical nature of most of the races in Star Trek a couple of times. In the television universe, there was an episode that was a treasure hunt, to which many dominant races believed would be a great weapon of some kind, that turned out to be proof that the major species were related and 'seeded' billions of years ago by a powerful omniscient race that had left the galaxy.

This follows the plotline of a book that was written as a sequel to the episode in the original series, City on the Edge of Forever. The Gateway of Forever, a time travel device, was also a remnant of these ancient powerful beings, and the seeding of the galaxy was also discussed there.

I tend to agree with most people's belief that DS9 and TNG were both strong (intermingled with some moments of weakness). Voyager had good ideas at times, but was generally trash, and ST : E was tragically cut short before we even knew what it could be. It might be worth taking a second look at TOS. I am amazed at the quality of some of the writing on that show, and the quality of production (considering the budget) is at times quite astonishing. Star Trek has been chasing the chemistry between Kirk, Spock and Bones, since that first year.

Edit : Sorry, sort of misread your meaning. The thinly veiled parallels to various people throughout history was something I actually liked. Romulans being Roman, and such. It added immediate backstory to each race. TNG got away from that, and made everyone similar. Klingons were angry humans, Romulans were political humans, the Borg was Apple. The Federation was clearly American, but I think the perfection thing was more an indication of Roddenberry's future vision of the human race. The Federation as American in today's world, transposed onto Star Trek, would be a much more interesting animal.