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.
The 6th season wasn't the ebbing and flowing. The story arc started with the final episode of the 2nd season and ended with the final episode of the 7th season. It ebbed and flowed through five seasons. The Klingon Civil War arc (my second favorite arc) started at the 23rd episode of the first season and ended on the first episode of the 5th season. That's probably the next longest but it didn't ebb and flow nearly as much.
And Roddenberry didn't like story arcs, period. He didn't want events from one episode to "bleed into" another. He wanted every episode to be completely self-contained. The particular length of this arc he would have hated. And think of all the things that happened in this arc. My favorite DS9 episode is The Die is Cast and there was a lot of stuff that happened before that and after with this arc.