I can see why some people consider this visual novel as a masterpiece, and I kind of agree that it has a really well crafted narrative structure, but I could also see some flaws on it that didn't allow me to fully enjoy it.

First (and the most obvious one I'd say), the immense amount of gruesome nsfw scenes that were threatening to take me out of the story in some of the chapters. Using topics like rape and bullying as character development feels kinda cheap to me.

Second, the philosophical facts. The story acquires a lot of depth due to referencing and entwinning multiple philosophical works which I admire and enjoyed finding out, but at the same time it feels like sometimes there's too much philosophical 'gibberish' that isn't really fully justified by the story, as if the author was sometimes dropping some random facts that are completely unrelated using the story as excuse (it's only my impression only the author knows about its real meaning).

Third, the End Sky II ending and the final dialogue. I truly liked that the full narrative of this visual novel is very open to different interpretations in both structure and philosophical meaning and this ending killed that mysterious vibe for me a bit. In my opinion, it wasn't fully necessary in this case to end up explaining the structure of the chapters and the general picture so much to the reader. I'm more a fan of letting people figure out things by themselves, which the final dialogue tries to do but ends up over-explaining too many things.

Besides these points, I think it can be an enjoyable visual novel for some people and I would agree with who labels it as a classic in its sub-genre (denpa?), but I fail to see how this work is better than some other visual novels I've read before that explore similar subjects. Writing is important when creating visual novels, not only the story structure, and I think this novel focuses too much on the latter and neglects the writing quite a lot.