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FWIW, I think this was specifically targeting AAA games. I think the author's point was that AAA games all have such milquetoast stories than an indie game focusing on just average storytelling skills can differentiate itself from a AAA game. That said, I'm just speculating. I'm a fan of the author's games myself, even though they're all SciFi/Fantasy.
Admittedly, I don't have a rigorous definition of what AAA means, but Myst was one of the biggest games of the time. Monkey Island didn't come out of nowhere. Neither did Planescape: Torment, or Final Fantasy 7.
I'm starting to believe the article is flame bait, hanging from a definition of "good writing" that doesn't hold with books either. "distinctive, individual, human voice". If Portal 2 isn't that, then Hitchhiker's Guide to the Galaxy isn't good writing either by this criterion.
I would say, in general I agree with this article. Of course, it's a bit hard to even fit some games into the description.
What is the story of Skyrim? The main story arc? Then hell yeah, he is right! But what about all those side quests? Some of those are at least different.
What about games which don't have a story like almost all the multiplayer games people love?
But yeah, in general, the stories kind of suck. They suck like the stories of most action movies or superhero movies. They are so generic I usually either cannot remember them or cannot tell them apart.
Regarding Myst, which I really like a lot and I have played everything up to Obduction, let's be honest, the story is kind of crap. There is a guy whose sons where dicks so he imprisoned them. That's it. Depending on the ending you get you either free one of the sons and get imprisoned yourself or you free the guy who accidentally also got trapped.
And Monkey Island? Great game! But the story? Isn't it just "guy meets girl, girl gets abducted, guy needs to defeat big bad and rescue girl"? I mean, you don't need a lot of story to make a good game, I think that's his point about Subnautica. But I feel like Monkey Island is just another example proving his point.
That's a bit of a harsh take, especially coming from a creator of a game. I'm not sure how one can come to such conclusions, except by having limited exposure to games. I've noticed that all the titles listed here were rather similar - 3D, action-focused. Those need a particular kind of a story.
The one outlier here is Portal. But it's by no means extreme. Go further, and you reach proper adventure games. Monkey Island? Myst? The Blackwell series? (Okay, I only played the last one, but the writing was on par with decent books.)
Go further and you get less gameplay and more reading. To the Moon has a story that's based on the same premise as one acclaimed movie (can't say which without spoiling). Keep going and you reach interactive novels like Her Story. Maybe it doesn't contain a lot, but after playing it I felt as if I watched a David Lynch movie.
What makes writing good anyway? Believability? Attention to detail? Uniqueness? World-building? Stirring emotions? I'm sure I can find a game that rises near the top of each category... except maybe uniqueness. Ubik is unbeatable there.