20ga has less recoil, and less downrange energy (800ft/lb@200yds in 20ga vs 1200ft/lbs@200yds for the 12ga sst slugs)

But seeing how 200 yds is pushing the envelope for slugs anyway, that may not be a real disadvantage. I would not want to go any lower than 800 ft/lbs for deer.

Its been rumored that 20ga slugs are more accurate, which was proven wrong by outdoor life this fall.