I agree that intonation matters a lot; I guess I'm thinking about how you'd make a notation that better conveys the information already there in the current scores, which is 100% equal tempered. I actually like the idea of modifiers for microtones, and presumably any of that stuff would work just as well on a 12-tone staff.

Also, with a 12-tone staff plus shape notes, you'd get a little extra information for just intonation because you can tell for sure what key was intended for a given note.