I think I made a post similar to this. One of the most irksome aspects of Star Trek fans who want the utopian future, is that they don't understand the cost of it.
First off, the entire setting is based on a peace created after the "Eugenics Wars"
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This seems to be a recurring theme in Roddenberry's repertoire since a project called "Earth: Final Conflict" based on his notes describes a situation that is an inversion of "First Contact" with the Vulcans.
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Interestingly enough, the "Taelons" whose enemies are the "Jaridians", are both descendants of the "Atavus". This is similar to many Star Trek plot lines including The Dominion, from Deep Space Nine, or the episode from TNG wherein we find out all aliens in the franchise that walk around upright like the Klingons, Vulcans, Humans, etc. are descended from a common ancestor.
Ironically, Roddenberry clearly did not believe that the fantasy utopia he wanted could come without a cost, and this wanton optimism towards the complex ideas he was actually forwarding through the creation of Star Trek and it's Federation is more of a dark warning than it is an optimistic view of the future.
Mike Stoklasa calls the original series of Star Trek "A horror series." The optimism of it comes from the outlook of those involved. The idea of an actual Enlightened person in Trek is someone who is able to move past petty grievances. Once again, as I've mentioned before, Bob is not one of these people.