The individual paths are actually going to get narrative priority. If anything I'm kind of worried about how to get the harem ending to fit around those arcs while still telling the same story, but I have an idea in mind for how I'm going to make it all work.
That's good to hear. It's a big challenge, though: the few games where harems seem plausible to me involve highly unusual settings, like the post-zombie apocalypse scenario in _Now and Then_ where social conventions entirely break down in believable ways.
The issue for you is that, having created a fictional culture that clearly anticipates monogamous relationships (you seem to be doing that, anyway) how do you also create a believable set of circumstances that allows the MC to screw _everyone_ without consequences... from the perspective of every woman in the harem?!
That's when harems become farcical: it's one thing to imagine an unusual situation where a couple women tolerate a poly amorous relationship... say, because the two women like each other (and the MC) a great deal. It's another thing entirely to imagine a large community of women trashing social mores and getting together with a man and a bunch of other women who they might hate.
But my view tends to be an outlier... most people seem to like the idea of even absurd, implausible harems. To my mind, though, harems usually tend to be incompatible with compelling NPCs/women characters... it necessitates that all the women involved make unrealistic moral and personal compromises.
Personally, it makes more sense to me to pursue individual stories with cheating options... or a few 2-3 way relationships, rather than the MC+all the women in the village. That is, in part, because the mere existence of the harem option undermines the strength and power of the female characters' feelings and agency.