I had similar issues with the finale to DS9 as I did to the Battlestar Galactica finale (both, not-so-coincidentally, written by Ronald D. Moore): both are really stirring and emotionally satisfying finales destroyed by really half-assed/pretentious conclusions. I can just see the writers room now for "What you leave Behind...":
Writer 1: "Wow, we have 1:40:00 of pure awesomness. We resolved the Dominion War, we gave each character a proper send-off with a touching farewell speech, and we got it all done just in time for tomorrow's 9 AM deadline!"
Writer 2: "Yeah....oh crap, we forgot about Dukat! Quick, to the Batcave!"
*5 minutes later*
Writer 2: "Ok, Dukat unleashes
Zuul (Not Safe for Work), and then Sisko kills him. And then he becomes a God...some...how. Oh well, off you go!"
To Deep Space Nine's credit, at least its rushed conclusion was only the last 20 minutes, not the entire second hour like Galactica's finale suffered under.