I've told people from the beginning to not worry about the points. There are and there will be differences based on some points. Some points are there just to screw with people. If I had my way I'd keep the "walkthroughs" off the original post, because they're simply going to confuse and frustrate people. If you're worried about the points you are playing this game wrong.
The player will have an impact and will have a lot more choices coming up. But it's going to be a while before the MC really comes out of his shell.
The story is indeed devoid of much of a plot. It's a slice of life VN. It's about the characters and the relationships you build with them.
First, white bread can be fucking delicious. Second, your MC will come out of his shell at some point. There
will be payoffs. But the buildup might be a bit frustrating for the impatient.