SPOLIERS (obviously):
I believe your review of this game isn't very fair. I don't think the point of this VN is the plot, but rather the character building. The development the MC (or Marco as he's named) and Amicus is the reason it's so highly regarded. The plot serves, as flawed as it can be, to guide these two through emotionally taxing experiences to bond them further. You've read the VN, you know what they go through, so there's no need to elaborate on what they do. While looking at this game from a critical point of view can make it seem mediocre, the heartstring tugging the game pulls throughout and ends on is plenty enough for many to love this game and for it to deserve to be considered good, or even great. I highly recommend playing through again, instead putting yourself in the shoes of the characters versus simply going in initially with a critical viewpoint, because that's a surefire way to immediately not enjoy something.
My viewpoint however does not mean I do not see your points in the flaws of this game. Your analysis of the flaws are well thought out and make sense to a great degree. I like your criticisms. But I implore you, if you go into things immediately critically, it'll be hard to see the good in things others see.