In one of the behind-the-scenes featurettes they talk about their creative process. Basically, they explain how they came up with ideas about cool set peace scenarios first and then they tried to build a game around those scenarios. That's exactly what it felt like and I don't mean it as praise. Uncharted 3, to me, is a bunch of, admittedly, really cool and technically impressive set peaces, held together by a somewhat disjointed plot. The pirate section is the perfect example. Very neat concept, fun to play and a technical showcase, but it comes completely out of left field and feels tacked-on story-wise. The game lacks the cohesion of the second installment, which makes it less enjoyable overall, even though many of the individual elements are objectively improved.

I read online that the actor who plays Cutter had to leave the project early due to his schedule, which lead to the story being rewritten last minute. Maybe it would have turned out better, if it hadn't been for that. Maybe not. Either way, Uncharted 3 is still lots of fun - it's just not as good as Uncharted 2.