It isn't a paradox. Star Trek is entertainment, first and foremost, and conflict is entertaining. Gene Roddenberry may have wanted to portray a post-human utopia of luxury space communism, as it were, where humans all evolved beyond their base desires and vices and everyone was a paragon of superior intellect and virtue, but no one wants to watch that all the time. His ideal of the perfect Federation human was Wesley Crusher, the most hated character in Star Trek history (long before the identity politics around hating the new Star Trek series came about.) People want dogfights in space and snarling Klingons and scheming Romulans. Drama and violence. Sturm und Drang.
>Is there anything else that isnt dystopia?
There is no utopia or dystopia. Star Trek was never very utopian, except maybe on paper. Idealistic and hopeful, sure, but the struggle for liberation from an oppressive order is by definition idealistic and hopeful. Star Trek doesn't become dystopian when it bothers to examine its own ideals, or acknowledge the flaws in human nature, nor is it utopian when it pretends they don't exist. I think that looking at science fiction in terms of utopia and dystopia is missing the forest for the trees. These are two opposing and impossible ideals, while most stories (excepting purposely grimdark stuff like 40K) take place in the middle.
And that's fine. Humans can't aspire to perfection, but we can be inspired by the struggle to be better than we are.