You know, I was considering naming that as a possible “main plot of the series”, and you are right that it’s definitely one of the main threads of the show, but then again, it feels very loosely connected, often even half-abandoned, and mostly not like a deliberately planned plot.
There are ebbs and flows, but it is the constant from which all the other plots of the series emerge. RHW admits that in the beginning, the writers relied a lot on Sisko being a dad as the element that distinguish DS9 from TNG. Then Jake grew up, and he became part of a different story with Nog. The Bajoran thing became a problem for the studio, so the writers shifted from politics to religion. More importantly, Sisko's own support for Bajor was subsumed by his relationship with Kira, whose relationship developed an unusual richness. I think there are some indirect references to development on Bajor, but almost all of it was off camera. The Dominion War became a major emphasis in the latter seasons, but just as often as it was a struggle to preserve the values of the Federation, it was a struggle to allow Bajor to evolve on its own. I don't think it was a mistake that the writers had Sisko choose Kira to help Damar, in a small way handing over the baton. In some way, it's Bajor, it's values as they have been cultivated with Sisko's help, that symbolically wins the war. And the series starts almost as it began, Jake staring into space with the woman whom Sisko helped realize her potential.
Where it becomes difficult to see is Bajor itself waning from the story. It's always there in conversation, but seldom visited. The number of new Bajoran characters drops of from season to season. There is an uptick in season 7 with Covenant and the monk who roots out Winn. But if I am not mistaken, there is only one new character, a woman vedek,who kills herself by the end of the episode during the six/eight episode arc. They went through a long story in which the Bajorans struggled against the Dominion alone on the station without creating continuing Bajoran characters.
ETA: Wolfe admitted that most episodes are indeed stand alones which have had "elements of continuity threaded through them." They were always taking stories from whatever source and developing them to suit their needs. But that means the first serialized element was the Bashir-O'Brien relationship, a long term project that Baer evolved by tweaking elements of numerous episodes.