"Not the best" in an understatement in my opinion. Save transfers can be wonky, you cannot access all content from a single program, and so forth. I'd rather have the inconvenience of a huge download once than to experience it again and again while playing.
While not the best it would likely be the easiest and straightforward option.
Im not defending it, just explaining it. Id prefer a patch/addon functionality but due to the engine (renpy) i have doubs on it even being feasible.
Given the design and build of this game I don't think the chapter route would work with how content is being added. Individual storylines are being added/expanded for the girls and staff which when added can be played individually but if playing a brand new start, as either a new player or just wanting to replay from the start those additions can be played/progressed simultaneously in a similar way as to progressing main/side quests in games such as Skyrim/Witcher 3 etc. I could very well be wrong. It's just my gut feeling.
The "build" of the game is already split into chapters if i remember, segmenting milestones between chapters wouldn't actually be that hard.
Transferring to a new chapter/EXE for the next chapter would be a X number of times change for a full play-through. X being the number of chapters. There wouldn't be any back and forth.
But this is all speculation, not the best option but an option.
To go on a wild one, heres an idea bomb.
The game could be split into seasons, the current game definitely feels like summer. Maybe the next could be autumn or winter.
Fully different weather to give a complete shift in everything. Having to close the lake for health and safety, students asking for it to be open for ice skating? Hiring an skating teacher? after school club?
Dressing sexy but cant dress too sexy due to cold (internal conflict) lol.
Potential for girls to get colds?
hot coco and movies every night!
Snowball fights and snow down the cleavage.
HM cant look through the windows at night due to the weather and has to push for dorm entry.
The potentials are nice to think about atleast. Allowing large changes to the norm with little contextual issues.
And again, not trying to push the idea.