I posted the question, but haven't answered it yet.
While I have problems with it, I didn't hate TATV as much as most people and in fact thought aspects of it were pretty cool. But I know that a lot of fans were really distressed by it, so for that reason alone I might consider it - it's a sore spot for so many.
Other strong choices:
Let He Who Is Without Sin.. the episode that represents everything I don't like about where the writers of DS9 went with the Worf character.
Shades of Gray simply because, technically, I would be removing less original material from the Trek universe than with any other episode.