Normal throws are still useful in notation for things like safe jumps and frame traps.
Personally I like > and < for directions, and - if you want to be explicit about neutrality. I usually prefer numpad notation for directions, but I don't think those make sense for this game.
Since J exists for jump, perhaps G (i.e. Ground) can be used to indicate landing.
As for the comma, I like it to be indicative of your character returning to a freely actable state, while adjacent characters are indicative of cancelling. xx is traditional for cancels, but is it necessary?
Setsuki's standard combo: >JCAG,AS
Jaina's anti air: >A,>AB
ch for counter hits? Why not !
Geiger counter hit combo: !<A,AC
Holding a button? How about |
Setsuki reset: JS,A|C
And maybe ; for cancelling a move late?
Grave super meaty cloud: <A;|B
Just throwing some ideas at the wall (maybe I've been doing too much code golf. Just be glad I didn't start suggesting diacritics...)