Multi-Scale, Sand Throw, Swift Swim, Chlorophyll, Guts, Regeneration, Mischievous Heart, Speed Boost, Magic Guard, Unaware, Flash Fire, Herbivore, Lightningrod, Storm Drain, Encourage, Shadow Tag, Magic Guard, Serene Grace, and Technician are just a few abilities that stick out to me as nice to get rid of if the Skill Swap user is able to do it safely. There's also Bad Dreams if Darkrai manages to hang around, though I doubt that.
But "if the Skill Swap user is able to do it safely" is a pretty big catch in the first place. Looking over the list of users, only Dusclops, Dusknoir, Starmie, Mew, Celebi, Deoxys, and maybe Bronzong/Uxie/Cresselia stand out to me as Pokemon who can take a hit pretty well and don't get such huge benefits from their own ability that swapping it away is a huge risk. (e.g. swapping Natural Cure from Chansey/Blissey or Magic Guard from Rankurusu/Shinboraa is a dodgy idea).