I think DS9 really straddled that line between story arcs and stand alone episodes quite well. I really didn't start watching DS9 heavily until the Defiant was introduced, and then when Way of the Warrior aired, I was hooked for the rest of the series.
I think if you can find a way to balance between the overall arc, and plenty of stand alone episodes, you can have a successful following, but it is so fine a balance to strike that few actually achieve such success.
Many say that Ron Moore's BSG lost its way...that it started suffering from scattered writing. I really don't think this is the case. Loved the show from miniseries to series finale.
I think it saw a decrease in viewership for the very reason that had been cited here....it was a highly serialized show, and later on it would be very difficult to catch up on while on its run. It seems to be enjoying decent DVD and blu-ray sales though. I have the entire series on Blu-Ray....and WOW is it amazing to watch in that format.