Mass Effect 2, definitely.
Don't get me wrong, both were great games but while Uncharted 2 was just Uncharted on a bigger scale, Mass Effect 2 actually felt more like a sequel.
Mass Effect 2's improvements were just so much more significant to me with fixing all the glaring technical issues and the streamlining of all the systems just made it so much better. Uncharted 2 felt more like polish rather than such a drastic fix (which could say more for Uncharted).