If it doesn't make sense to you, it's not anyone's responsibility to spoon feed you, especially not the developer's. The purpose of any story is to take you on a ride and engage your mind. If it tells you everything and spoon feed you with all the details, your mind won't have to do anything. It's a similar problem to AAA roleplay games where the developer shows you where to go and what to do and people have gotten used that mindless way of playing.
The story does enough to take you in. The rest is up to you.
Now I agree that the story is not incredibly flashy, just a teenager living with two women and goes to school. But I've played other visual novels where the dev goes into insane amounts of details and the problem with that is that you start to feel the dev behind it, especially in the MC. And that's just disgusting, cringe, and unnerving, even if the story is awesome and interesting.
This is the way to make visual novels. I agree that the experience can be much better but not in this format. And not with renpy or similar softwares
