Skane, that was really a great read, and thank you for clearing up what Nayuki's arc is supposed to be about...as much as I've looked around, I never found a clear explanation of the significance of her sleeping habit, yet I just KNEW there had to be something more to it.
As another person who was least interested in Shiori's story (although perhaps more interested this time than in the Toei Kanon--and I liked her lots more this time around), I do have to point out a subtle but important role Shiori has that is less obvious the second time around.
Shiori is something of a (good and deliberate) red herring. Kaori's lack of acknowledgement of her existence in turn plunges the viewer into speculating any number of possible supernatural reasons for this, after the prior arcs setting this up, and in turn when her real story demolishes those theories, she helps keep the viewer from assuming that all solutions to each character's mysteries will be supernatural. I think this is a really important role when viewed in this respect, as it keeps the viewer guessing and skeptical. Of course none of that is true if you've already been spoiled the story from the game or the prior series (though I know it was true watching the first series and I suspect might have a similar effect in the game).
Once I get a PSP, I'm definitely going to order the portable Kanon and Air now...I really want to bring it full circle... ^_^;