I actually thought the story in Uncharted 3 beat the one in Uncharted 2. More realistic setting and more believable characters. It didn't really rely on 'supernatural' mysterious... stuff, which I thought was kind of lame and unnecessary about Uncharted 2.
However, Uncharted 2 was obviously a way more polished game in level-design, gameplay and in the technical aspects, and better because of it. I'd vote that as one of the best games of the generation, so my vote goes to UC2.







