Ok, I have a really good theory. (Spoilers for Air, Planetarian, and kind of mostly every single KEY VN, Anime, etc.?
What if Yukito, after he died, actually became a God and helps everyone in need. Ex. Glowing yellow light in Clannad and Air! Also have you noticed that all of KEY's work has... Air and a sky! Coincidences? I think not! Also maybe in Planetarian, maybe Yukito was actually ashamed that everyone fought and the world ended, so with his Godly powers, he made the Earth covered in grey clouds and rain for many years.
This is a joke and is not meant to be taken seriously.