In Kanon, I never understood why a fox was shown at the end because I thought there was a lot of evidence that Makoto was dead. But then I realized that Ayu's miracle healed everyone else, so why wouldn't it bring Makoto back? It was never stated it was set only to the living. —swtrooper42
Preventing death is one thing, genuine resurrection is quite another, and it's unlikely that Ayu's miracle could have done anything about that (even without the game's implication that it only works on one thing at a time), especially considering that Makoto was, in a sense, already dead. But guess what? There is someone who we know can bring people back from the dead...Mai. And guess who told Yuuichi that Makoto was going to need him very badly...?
In Kanon, by default, a window appears in the upper left telling you what the date is. But there's a period towards the end of January where the window doesn't appear, and you also don't get the eye catches telling you when its a new day. It took this troper a while to realize the significance of this: Yuuichi is so engrossed in taking care of Makoto that he's lost track of time.
Kanon seems to be about restoring connections that were made during childhood, which makes Shiori seem out of place compared to the other heroines as she does not have any connections to Yuuichi's childhood. However... from another perspective, Shiori's story is still about restoring a relationship she had in childhood that was since broken: that with her sister. Viewed this way, Shiori's story fits a bit better with the rest of the heroines'.
Looking back at the scenes with Ayu Tsukimiya and the taiyaki shop owner, you may ask yourself, "Why does Ayu run away whenever the owner shouts at the cat (and later a dog), even though she's 17 and should know better?" Here's the thing: she's been in a coma for the past 7 years. This means her body may be 17 years old; but mentally, she's still a 10-year-old. She cannot tell whom the owner's anger is being directed towards, and just like every other 10-year-old in this type of situation, she makes a run for it simply because she's scared. This also explains her glomping and crashes into hello with Yuuichi because it's natural for 10-year-olds to greet loved-ones this way.
Also, some people have pointed out how the demons didn't appear during Mai and Yuuichi's supper -> to sex scene on the school desks. Makes much more sense when you recall that these demons come from Mai's own suppressed powers — she unconsciously wished for them to not appear as she and Yuuichi had such... intimate moments, so this wish "cockblocked" them from showing up.
Kanon is set in January. January is fox mating season. Convenient (creepy OOC conduct in Makoto's route aside). Furthermore, during this time, female foxes rebuff or even attack male foxes coming onto them, except for a period of about three days when they suddenly become not only receptive but outright flirty instead. No wonder they made Makoto a tsundere.
Kanon is a romantic Visual Novel. You play the protagonist Yuuichi, who at age about 16 is returning to a town which he used to visit frequently until 7 years ago, but has mysteriously little memory of that time. According to the choices the player makes, Yuuichi falls in love with one of five heroines, finds out how his past is linked to hers, and rescues her from some horrible fate through his love. But wait a moment - that means the other four girls are NOT fallen in love with and NOT saved from their horrible fate. Hence whatever you do, at least three of them will end up dead or in a permanent coma.
Ayu probably remains in a coma for the rest of her life, or at very least for a long time.
Makoto, having sacrificed her life (as a fox) for a few weeks as a human to get to know her one-time rescuer, is rejected by him. She wanders out onto a hillside and prematurely freezes to death.
Mai: Her one true love from childhood returns but either never meets her or pays insufficient attention to her. She probably gets killed by an invisible demon created by her own mind.
Shiori dies of her medical condition, rejected by her sister who can't bear to watch her die.
Note, the same can be said for pretty much any Visual Novel that involves branching storyline (i.e. 99% of them). Which makes the simple act of choosing to do ANYTHING a Sadistic Choice. Although in most cases, the other characters and their associated problems are simply treated like they never happened and pushed gently away storyline-wise.
This is probably why CLANNAD, a later Seasonverse work, introduced the concept of "variations" (a multiple-worlds concept similar to "fragments" in When They Cry) and had its hero go around saving everybody. And hey, at least the anime adaptation saved them all, though Makoto's still got that Bittersweet Ending.