The franchise's creative director, Amy Hennig, believes Naughty Dog are kind of ahead of the pack," when it comes to motion capture in games. And that's the fundamental difference between Uncharted and other games. Well, aside from great writing and brilliant performers of course.
Apparently, that wasn't always the case though. Hennig explained that the motion capture studio used for Uncharted: Drake's Fortune was "an outdated, uncomfortable place to perform, equipped with a camera array that painted the room with eye-searing red light. Apparently the studio's poor acoustics also made it impossible to record dialogue at the same time, something that had to be added later.
But the success of the first game allowed Naughty Dog to upgrade for Uncharted 2: Among Thieves, fundamentally allowing the studio to record dialogue while the actors moved around. Naughty Dog has now invested in its own motion capture studio for Uncharted 3, allowing the team to record several times a week.