So the story is not set in a post-apocalyptic setting? The story does not focus on asking the player if he is on the right side of the conflict? The story has no focus on sexual innuendos and trying to appeal to male audience? The story does not feature any gloomy, brooding, mysterious characters?
***Apologies, Spoilers follow for rebuttal purposes***
Well considering its a sequel to a game with a post apocalyptic setting... its technically post, post-apocalyptic.
The point is, and this goes for Nier also, sometimes there is no right and wrong side. Just competing interests and agendas. So your simplistic "good guys and "bad guys" description is precisely the thing that Yoko Taro is deconstructing.
There's very little focus on sexual innuendo, and given the importance of 9S to the story, I doubt its aimed at a specific gender or romantic interest group. Yoko's works tend to include characters of all genders, gender-statuses, and sexualities because as he's spoken of in interviews the world contains a diverse range of types with "normal" being merely a synonym for what's most commonplace.
But in any case. what any story about is not just setting and basic character tropes. Its about theme, issues, and authorial intentions.