If you could take any one kingdom card and wipe it out of existence, which would it be?
Well the card that I could change in order to improve its set the most is Scrying Pool (dropping the Spy part), but I wouldn't get rid of it, just fix it.
The card that has the least going for it overall is Saboteur: it's an attack that doesn't give you resources, which seemed fine at the time but it turned out people don't like that and it's not like there's any reason I need such cards, yes I still made Sir Michael; it's an attack that trashes cards, which I think are worth making in moderation but they have to really please the people that enjoy them, since some people hate them; it's weak, so it's doing less for the people that might like it, and contributing less to possible strategies in a game; it's wordy; and Intrigue already has a trashing attack that makes resources, is strong enough and fun enough to be worth doing, and it even manages to be simpler.
The card that I personally acquire the least often is Secret Chamber, and it causes rules confusion too. I would certainly replace both cards if I were working on Intrigue today.