Killzone 2 was a game with very strongly developed squad gameplay, meaning much of it involves fighting battles with 1-3 squad members assisting you. However, due to the expense and difficulty of such an endeavor, the developers did not add a feature where humans can play as the squad members with you (campaign coop).
Meanwhile, BioShock is a game where playing alone is an essential part of the story and adding coop buddies to the game would make no sense narratively, even if they could make the gameplay aspect work.
Coop "would make sense" in KZ2, so it gets dinged for lacking coop. Coop "would not make sense" in BioShock, so no one criticizes it for lacking coop. Yet adding online coop is roughly equally demanding/expensive for both teams. In a way, a gameplay style / narrative choice on the part of GG opens them up for criticism for not doing even more with that choice -- while Irrational avoided the criticism simply by not making a similar choice.
Is that fair? No. Not really.
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Uncharted is a game where the main guy has an everyman quality, sort of a "normal" guy who doesn't seem like a gruff soldier type. Because of this narrative choice, it is expected by (some) reviewers that the gameplay wouldn't involve him killing hundreds of baddies.
Meanwhile, Call of Duty is a game where killing other humans fits in narratively perfectly. So of course it gets no criticism for being a human-killing-heavy game.
Is that fair? No. Not really. ND did a nice thing -- introduced a relatable everyman character that really strikes a chord with people. In doing so, they were unable to somehow change the rules of modern-set action games, wherein shooting/killing is pretty much the way to provide the gameplay "meat." For this nice thing, they are rewarded with the mass-murderer criticism which 99%+ of other games involving killing don't get.
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Don't get me wrong. The above reads a little bit like "oh, poor Naughty Dog." Putting it all in perspective, of course, the Uncharted games are very well received critically, despite the frequent dissonance attack. I am merely responding to those that specifically DO criticize them this way. They are entitled to their opinion, of course. I just don't think it's quite fair.
On the other hand, though, the bottom line to a reviewer should be how a game makes you feel. It's not necessarily about "fairness" the way I described it. If the dissonance honestly bothers you, then mentioning this in the review and scoring it accordingly is the right thing to do.
...but I am surprised it bothers people this much. It's not like what Nate and co. do is immoral. He kills pirates and mercenaries working for bad-to-horrible people. The alleged dissonance is the ease with which he does all the killing, seemingly without bothering his conscience. However, why isn't this a problem with any number of goon-killing wise-cracking heroes, chief among them Indiana Jones? I've even always thought that Indiana Jones films were considerably meaner and more gleeful in their depiction of violence against bad guys than Uncharted is. The body count is higher in Uncharted, but that's because it's a long game vs. a film.
So yeah. This criticism has always seemed both unfair and, if fairness is not a concern, unreasonable to me.