This is one of the major things that make me believe in Evil Susie/Altered Prophecy Theory. Originally I imagine the prophecy was meant to be about Kris and Noelle's relationship, so the whole "Love finds its way to the girl" thing would've been the culmination of their journey through the Dark Worlds together. Just about every single Dark World has some sort of connection to the games that Noelle (heavily implied) and Kris used to play "King on your side, Queen on her side, Tenna in the back, it was Chaos! Chaos!"
Think of things like this, if Alphys had originally run out of chalk and needed more, she probably would've sent Kris to the closet, as he was the last to arrive, and probably Noelle as well, as the student closest to Kris to make sure Kris didn't fuck around. But instead Susie shows up at school that day (Which is itself, apparently uncommon enough to surprise Alphys). Naturally, this confuses the fuck out of the prophecy, so Susie, now in the role of the Girl knows she should fall in Love, but doesn't know what Love even really feels like. Meanwhile, Noelle, who should have been the Girl, and should have fallen in love has an unhealthy obsession with Susie. So what should've been a culmination to something, instead feels like something that's just wasting time.
Either Toby is a total fucking hack, or he's deliberately writing a romance that doesn't make sense because destiny demands it.
It could... honestly be either.