speaking of which, what do you all think... had a super natural element been introduced from the start, would the story have been more coherent and made more sense?
No, I think that's the last thing this needs.
if not, what is hurting the story
Completely unlikable, opaque characters.
and what could save it?
Characters that don't make me want to straight-arm them through the wall for their distinctly bland mix of vapid, petty, and thoughtless. This looks like it's going to be one of those things where the only characters I like are side characters. The way it jumps around, the main characters only have that much development anyway. It's sort of damning that I can't even remember ANYONE'S name.
I'll keep reading for the excellent art, and I appreciate that someone's working on it, but it could seriously stand to spend some time developing one character. Like, say, the main one. (It feels like even StoPani gave Nagisa more time to bake than this girl is getting.)