Well they aren't entirely different games. Both take from the RE4 style of play and adapt it like so many other games have, but they have 2 totally different purposes as game. The argument almost seems like Mass Effect has these things while UC2 never had any attention of having those things and therefore is worse because of it. I would be like discrediting Halo in comparison to Mass Effect because you cant' level up.
It's doubtful the narrative for Uncharted 2 was ever meant to be so character oriented as Mass Effect 2. But you could also flip it around, and say even if the Uncharted 2 storyline isn't that great, it does loads more than that of Mass Effect 2 which centers around characterization rather than a progressive and dynamic story line (something usual for RPGs although some still have some pretty good stories).
Point is, the comparison doesn't actually compare them but plays on a suppressed information fallacy. Lots of these coming from IGN lately. Obviously for hits and to stir the pot. Sad thing is, these things probably could all be very well done and thought out and provide insight into the industry and our own gaming biases, but it seems IGN refuses to put the work in to achieve such success.
