Holy shit somehow no one has mentioned:

Nier Automata

It counts as a masterpiece because of how well it blends game design, gameplay and story. I have played very few games as thoughtful, or that weaved the gameplay together into the story it was telling in such a meaningful way. I never thought once in my life that I would think philosophically about bullet hell but somehow Nier Automata has something profound to say and even manages to say it using bullet hell as a gameplay mechanic.

On top of all this, it also has a lot to say about classical philosophers, their works, and honestly deeply subverts things they had to say. It asks tough questions about their thoughts and ideas, once again, through gameplay. Numerous characters are named for classical philosophers: Pascal, Jean-Paul, Simone, Engels, Immanuel... (Yoko Taro obviously has feelings about how Jean-Paul Sartre treated Simone de Beauvoir.)

Further, Yoko Taro is doing something that a lot of game developers fail to manage to do: He is embracing gaming as a storytelling medium and eschewing the traditional three-act arc from film. Because gaming is not film. As Marshall McLuhan posited, "the medium is the message" and unlike other developers Taro's writing is aimed at the medium he is working in instead of leaning on the ropes and tropes of other mediums. (Referring back to above, tying the gameplay into the story, focusing on the medium)

It's basically impossible to not break down into tears at the ending.

Don't write it off because of the scantily clad anime women. Stay for the depth of the human condition. It is truly a masterwork in multiple respects.