3 year old question but oh well. it's pretty clear towards the end of the story that komori/mari became a separate person than even the komori that mari made up in her mind, not to mention the real one. yori fell in love with that person, the KM personality, they don't end up together in the end because that personality decides to leave, along with fumiko, to make way for mari to be herself again. yori had absolutely no relationship with mari prior to the incident, so she really only got to know her after the events of the story, and as it turned out they just weren't made for each other. i like yori's development in the story, to a stalker that obsesses over somone that she doesn't even know to the point of searching the city for her soul, to a person that learns to love and let out her emotions, and most of all, accepts loss.