Indeed. But i guess ND just wanted to develop the Nate-Sully relationship in this game. For example, Sully's in Uncharted 2 for, what, 5 chapters? And Elena is the main focus of UDF. Chloe is featured fairly regularly in UC2 but again, they probably just tried to delve into Nate's past a little more. It'll all change in the next one, i can safely say.
I think they were trying to be not as overt with the storyline as they've been with the previous two and then realized that they didn't really explain what exactly it is Drake was looking for.
I don't know. I really liked Uncharted 3. It wasn't quite as awesome as Uncharted 2 but it was still pretty **bleep** good. FWIW, the "Supernatural" part of U3 was done better than either of the previous two.