The Dominion story arc was the best of the entire franchise...and I loved me a Star Trek story arc. It was also the longest and the only one that ebbed and flowed. Imagine another story arc where the good guys lost as happened in this one. They lost the Deep Space Nine space station for the first six episodes of season 6. Nothing like that ever happened with another arc in the entire franchise. Gene Roddenberry would have HATED the Dominion story arc.
...but Voyager was my favorite show of the Franchise.
See I felt that it didn't flow. It started to ... and then ... stopped. They put the entire story line on hold for most of the season and part of the next season.
Roddenberry would have hated the way they did it. But he was all about social issues. If they had embraced that aspect, especially in the wake of Vietnam and shortly after the Gulf War, he would have appreciated it.