At first I felt UC2 was better. Then after really thinking about both games in their entirety, I came to the conclusion that they're both equally great, just in different ways.
Uncharted 2 had a lot of "wow" moments, and I think that's what a lot of people base their comparisons on because that's what they remember most. UC3 however, had a more adventurous feel to the overall story. I also feel that they're both equally flawed. The platforming in UC2 felt a little too magnetic, while the AI in UC3 was sometimes downright retarded. Um, excuse me bad guy, I'm half dead and reloading my pistol, yet you choose to run right passed me to hide behind a crate.
At the end of the day, they're both amazing games, and should be experienced by all action/adventure fans.