Hi The Naughty Captain, I just want to say you've made a great game. The multiple and overlapping paths are interesting and ambitious, the characters are well-developed and the sex scenes are super hot. I particularly appreciate the softsub/lovesub route. While I personally prefer the love-both route, softsub is something that is woefully underexplored in the genre of erotic VNs. Most VNs make a hard distinction between love and sub routes, and I love to see more of this grey area in-between. There's something unique about wilful submission - submission out of love, not manipulation.
However, the points system is the most obvious and largest issue with the game. The "rack up as many points as possible" game design for erotic VNs/games is one of the worst, only second to the "pointless sandbox to grind stats". I believe it's frankly an outdated system. Players aren't deciding "what choice do I want to make, or how will this affect the story?" or even "is this how I want to play the character?" but "which one gives me more points?" I saw in an older post you said you want people to play the game without a walkthrough. A large points system is a poor way to go about it because you're literally gamifying the system. So of course people are going to use a walkthrough to optimise points (god forbid you miss out on a scene by 1 point), or at the very least, liberal and excessive use of rollback. I will add you're hardly the only game to have this issue.
This is not to say you should have no points at all. The complaint is where almost every "choice" is just picking the dialogue option that gives more points, and you're pushing hundreds of points. A very minor points system for more important actions works fine. Compare a MrDots game where you get so many points it's meaningless and adds nothing to the game, to a PhillyGames game where each point is meaningful. Healthy use of flags is great as well like you suggest (though you've already clearly got some in place).
I don't know about making any changes retroactively as it's a lot of work. I think everyone would just prefer you keep moving forward and apply the changes in the future. If you remove most of the points then you make most of the choices completely pointless. I know some games have "graduated" their points systems where once you've reached a certain point in the story/crossed a threshold points don't really matter only specific choices do.
I'll end by saying I know I'm being critical, that I'm being an armchair VN developer, and that's true, but this is my honest, genuine advice to improve the game, and I recognise that producing any kind of media including an erotic VN is a lot of work, what you have already accomplished is a great thing and well above the standard affair of VNs that can be found on this site. Keep up the good work.