If I had to call it, I would say Mass Effect 85% and Uncharted 2 80% or a marginal difference.
Graphics? Uncharted 2 probably.
Visual presentation? Uncharted 2 probably.
Gameplay? Uncharted 2 probably.
Story? Mass Effect 2 probably, Uncharted 2's inconsistancy between cutscene and gameplay kills it.
Replayability? Mass Effect 2 due to the different paths you can take in Mass Effect 2.
Value? Mass Effect 2 due to the above and overall length.
The difference is that the areas where Uncharted 2 is better its close but where Mass Effect 2 is better theres a gulf. However someone with different values to me may make a different choice. It will be interesting to see how these games sell relative to each other to gauge the general public reception.