Yeah, I agree the author intended it to be Naru+Keitaro from the get-go (and I know how canon goes typically), but (as sometimes happens while writing a story), the characters have their own ideas. Ken was simply writing a more cohesive, interesting, and believable story in Motoko's thread. Whereas Naru's thread in comparison read like a 'single note' stubborn "gonna marry you because you're the promised one". So when the author wrenched the story back to his originally intended ending, my "
suspension of disbelief" was broken. My experience at the time in reading it was similar to one where the backdrop of the stage falls and we see the puppeteers jerking the puppets around -- it dashes the illusion the puppets are "real" and breaks the story.
If he'd left the Motoko thread less developed or more cantankerous, then going with Naru would have made a lot more sense.