One thing I would recommend would be to establish a kind of level of intimacy with each girl, we have clues but i think that with a level of intimacy or affinity it would be much clearer, and this could be a condition for a major event to happen for girls to have a certain level of affinity to directly relate the missions of each girl to the main story in a more direct way. It could also be put as a condition for future pregnancy. This way I saw it in the game Hero's Harem Guild and I think it would be something good to implement, it is just unna suggestion I hope you will get some new perspective on this.
If I remember correctly, there was something similar planned/partly already implemented which was later removed, well I dont know why dev removed it though (I also don't know if he will plan to readd them once the game has reached pretty far ahead).
This is my personal opinion, playing same content repeatedly just to gain some experience, doesnt represent they gained anything new, its the other normal events thats builds the relationship between characters, I consider it just waste of time personally. If the aim is to make people sit longer to complete the game, then its a good idea from the devs perspective (after all there are people who still says there is not enough game play so not why make them replay some loopy events).
And regarding the clarity for event clues, I would say that the some hints can still be improved at places and also some events should be locked until some evnts are not done. (dev has already done a lot of critical improvements in that case and still doing in each release), but after all it is just one single dev doing release consistently every month, unlike dev of HHG (no offense) who has not said a pre-planned release date, so he can work till everything is fixed and tested multiple times. So their method of implemntation is entirely different.
Of course there is a difference between someone who releases an update every month and someone who has been developing his chapter 1 for 1 year, obviously the last one not having a date on which to take out the game can take the time to try things and change or modify them, while for a monthly update game implementing a new mechanics can bring great problems as there is not too much testing time because this is done in parallel with the development of the content you cannot devote enough time to it. My point is not to compare the games but to give an idea of how I could get to implement what the events are from the relationships with the main events in a clearer way to my mind.
sorry if my English is not very good I am using a translator xd.