For example, in any Emma's path, it's important to have a huge time game between their discussion at the end of chapter 1 and their reunion again at the end of chapter 3. [...]
It's truly an experimental feature that might turn out to be a disaster and be scraped in the following update.
First of all, it's truly a remarkable 'lewd game' you're building up here, and I am duly impressed. The attention to detail in character personalities and affinities is like a real breath of fresh air, one that even makes me wonder if, like your MC, you are also a psychologist or psychology student...
The one slightly critical thing I might say at this point is that, perhaps for obvious reasons (making it possible for the MC to go any route for as long as possible), some interactions between the MC and the girls, especially in the middle/later stages (chap. 4, 5) sound contradictory, sometimes presupposing in different conversations that he does like, or doesn't like, one specific thing (kink, personality trait, etc.). It would seem that the main point in the MC character is (a) recovering from the guilt of his past behavior, plus the subsequent (b) trying to be a good person, and wondering if he can. I.e., remorse + confidence issues. That is easy to see in the Emma or Deb paths; however, he seems so bold with Leah while guiding her in her exhibitionist path, in a way that one would not expect to see from someone with these issues -- perhaps understandable by the desire to keep the Leah path an open possibility for longer (perhaps for dramatic reasons?).
And then there is his initial conversation with Kim in Ch. 5... if you did let her walk all over you, it seems to follow from that specific change in MC's goals; but if you didn't, then it seems to come out of the blue. Why would he express a desire to be 'walked all over' by Kim after having (the VN would have us believe sincerely) rejected her and claimed he'd tell Pete about her cheating as soon as he had the necessary evidence? I can see an attempt to make this a consequence of his scene with Emma (if he went the humiliation path and submitted to her 'new prank'), but I'd expect him to be quite smitten by Emma after it and to pursue her, to tell Emma that he would like to be a consensual doormat for her, not Kim.
All in all, though, this is too little to really worry about. You are producing an intriguing game, one that actually has me interested in the fate of every character (even the -- admittedly less well developed -- male characters, Carl, Pete, and Jamie). It's especially good to see MC having so much personality., rather than being an empty husk for the players to project themselves onto... I'm also quite happy with the realism you're placing into every path by making things look plausible in the real world rather than simply the stuff of fantasy (nothing against fantasy, it can be a lot of fun to inhabit strange worlds full of kinky women that can't exist, but it is refreshing to see a closer-to-real-life approach to this theme). I'm even wondering if you're trying to say something about the nature of kink, and the extent to which people should or should not pursue it (to the detriment of other aspects of their personality) -- i.e., whether it can be self-destructive rather than self-affirming as so many kink-positive people claim.
Thanks for the time you've already spent on this intriguing game, and I, for one, am looking forward to all new developments. (That scene with the three spirits in the cave was impressive, by the way. Kudos for that!)