Uncharted 2 is one of my favorite games of all time because it does such an excellent job in putting you into the role of Nathan Drake. The story isn't amazing or anything like many have said, but hey... neither is anything from Bioware, and yet I still love Mass Effect (1, 2, and mostly 3). I don't think you can put a strike against Naughty Dog for not reinvinting the literary wheel in terms of the story because that seems like a mighty hard standard to live up to. The characters are fantastic, the dynamic between Sully and Drake is top notch, and I haven't seen a game with better banter, one liners, and quips.
The game approaches movies in terms of storytelling. The story itself isn't great, but the presentation is fantastic. Avatar is Dances with Wolves with aliens, but I certainly have no regrets seeing the movie because it was a technical marvel, and told the story well, even if its a story that has been told many times.
If people really expect Metal Gear Solid level story in every video game, you are going to be severely disappointed in.. well everything not MGS. If you deconstruct anything Bioware related, you well see a generic story, an obvious antagonist, and a xanatos gambit at some point. But I found Bioware's games to be excellent in terms of character interaction, illusion of choice, and exploration. They are well-done, and allow me to appreciate the game while over-looking some of it's literary flaws.
Not everyone likes the same things, everyone has their tastes, etc., but it is a little disheartening when others use a measuring stick to declare why something is bad, when many of their favorite games wouldn't hold up to the same measuring stick. From that alone, it tells me that at the very least there is something else that bothers them about the game, not the stuff they list. If it was, they wouldn't like a plethora of things that they no doubt like (i.e. Bioware. We are all on the site, so i'm sure at some point we all liked one of their games). It must be lack of customization, linear gameplay, something...
All-in-all, Naughty Dog is pretty high on the list in terms of storytelling and story immersion for me. Their story might not be ZOMG amazing, but the sum of their work is excellent. Nathan Drake feels like a modern day Indiana Jones (one of my favorite trilogies of all time.. I don't count Crystal.. I try and forget it).