This has already been brought up and you can find info about the moonstones on CBTL wiki by searching for which girl you want on Cabin by the Lake
You are definitely right.
While making the game I have been at constant odds with myself over having mysterious elements that reward exploration for the player, and then having a game that isn't a confusing mess to play. Ideally, we could have both, but the more and more time passes, the more I realise that my head is up my own ass and I need to put important progression information in the game. The moonstone guide is in the works but I just haven't gotten around to it yet.