I also think that the Shizune route is perhaps the one that lacks the most significant link, for example. Do they want to tell us that the relationship with Shizune was just another courtship that ended when you graduated?
On Lilly's route, she places Hisao above her own family, and that's not something you would do for any boyfriend, as I already said, I think the couple that really complements herself perfectly is Lilly and Hisao.