Short version: Uncharted 2 is the best of the two.
Long version (spoiler free):
I thought UC3 started way too slow, so slow that I didn't feel like starting another playthrough when I finished the game. Also, they made the parts where Drake is walking through the desert way too long.
The story in UC2 is more enjoyable, Lazarevich is ten times the vilain that old English Lady is (don't remember her name). Chloe and Elena look weird in UC3, I don't know why they messed with their UC2 models which were perfect (except for Chloe's eyes).
The hand-to-hand fighting is not that good (it's square, square, square, the occasionnal triangle push or circle tapping, rinse and repeat). It wasn't good in UC2 either but you were forced to use it only once, in UC3 there's many occasions where you HAVE TO use it, it's quite boring.
(Slightly spoilerish if you don't know the set pieces already) As for set pieces for me it goes:
Shambala >>>>>>>> Ubar
Nepal Mountains >>> Desert
Cruise Boat >>>>>> Train
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