Kanade was never meant to be with Nanaki.
Yeah, I think I'm gonna pull a "Knowing Better" on this one (coincidentally, what I'm about to say is from his "Hitting Rock Bottom" video, so it's kinda fitting).
Technically, no one is ever truly meant for someone else. The fairytale idea that there's someone out there who's your soulmate and once you find them you'll be with them forever, is little more than wishful thinking. "Knowing Better" blames Disney for putting that idea into our heads. Instead, you find (and fall in love with) a person that fits most your criteria and make it work. In "Knowing Better"'s own words, Relationships are work. The way I see it, what's going on between Kanade and Nanaki is an example of both of them working to solve their own and each other's issues, albeit slowly, given how deep those issues are, as well as the fact that they're teenagers, and the relationship they're building requires a lot of work from both of them, and, as we've seen in recent chapters, some help from their friends.
Also, just in case you think that by referencing the "Hitting Rock Bottom" video by "Knowing Better" that I'm trying to argue either or both MCs have gone through experiences traumatic enough to count as hitting rock bottom: I'm not arguing that. Such a traumatic experience needs to happen in adulthood. It's not gatekeeping, it's just psychology and neuroscience.