uncharted 2 has better gunplay, set pieces, theatrics (buildings crumbling while gameplay runs in real time for instance), more variety, better sense of adventure, more moments that are defined solely by exploration, better replay value (reward/point system), an awesome multiplayer mode, and better graphics.
uncharted 1 gets annoying. You go inside a cave that hasn't been explored in like 500 years and all of a sudden a bunch of dudes with guns come out and start shooting at you. Every fucking screen -- guys shooting at you. No sense of variety, it's always the same gun fight, different location.
That said I'll take both Uncharted games over any other third person shooter that isn't Vanquish/Shadows of the Damned. Uncharted is the only western third person shooter with smooth controls with an agile character that doesn't control like molasses that I can think of. Very Japanese-y.