If Kyoto Animation were to go the multiple universe path, I think it’d be like…
- Universe 1: Nagisa
- Universe 2: Kyou
- Universe 3: Tomoyo
- Universe 4: Kotomi
I won’t list the After Story yet as that one will be fairly linear and easy to write a story for. Of course, Nagisa’s After Story will end up an extension of Universe 1. The only other extension that will exist is for Universe 3, and that would be Tomoyo After.
All the characters are covered using these four universes, so Mei, Koumura, Fuuko, and Yukine could be written off as secondary characters that help move the storyline; Ryou and Kappei is obvious; Misae is also obvious as well.
UPDATE (6/22): Based on the conditions laid out, Misae’s route looks like it’ll end up in Universe 1. Now Tomoyo and Kotomi have ended up independent. :S