The contradiction is in many people's minds. Historical trends and forces actually do make a narrative, if precisely what or even how many it is is very much a matter of debate. Nonetheless, oddly enough, people who will more or less insist that things just happen on a big scale will nevertheless force their own lives into a narrative. Since there isn't really a dividing line between personal life and "history," i.e., what happens to society at large, there are in fact larger narratives that include the personal. However, very, very, very little drama or literature is interested in realistically depicting people in context. Even though in the end that is the only "realism" that there truly is.
If you really think Kim acted the same at the end as at the beginning, you're just not seeing what's there. It's easier to miss since Kim was a minor character. A Vulcan changing is pretty much rewriting the concept. Chakotay had no real function after the electronic religion was dropped, and essentially became a minor character too. Expecting the captain to share an emotional life, given the hierarchical nature to Starfleet the show premised, is ludicrous. Janeway's role was fixed and that fixed what we saw. It wasn't as exciting as Sisko's character gyrations but much more realistic. Which is pretty much the real animus against Voyager, I think.
As for DS9's commitment to wish fulfilment somehow implying happiness, one of the most common fantasies is the suffering hero.