The biggest problem is that the scale is too huge.
I have no idea what they were thinking when they started making up ideas for this game, but there were several ways to make a fate game and that did not involve timetravel, singularties, and the fate of all mankind every single chapter.
And then for some reason, they choose to write 5 chapters in a row and are just simply awful. seriously, your anime adaptions are just straight up skipping the first 5 chapters of the story because there is nothing of worth in them. That is a problem.
It's now also been about 2 years ingame, and the protagonist hasn't even bothered to ask for a gun. having the crypters point out how utterly useless he is does not make it okay.