One additional idea along these lines is to make use of the already populated FATE areas where atmas cannot be obtained (Coerthas, Eastern La Noscea, etc.).
Q: Is it possible to create a random atma drop upon completing a FATE in those useful leveling areas and have it intelligently choose from the list of atmas that you do not have in your inventory?
So if you have atmas 1, 2, 3, 4, 10, 11, and 12 in your inventory and you participate in a FATE in a currently non-atma-dropping area, there would be a chance of dropping atma 5, 6, 7, 8, or 9 so long as you have a zenith in your inventory (or equipped). Coerthas is a big FATE leveling area and it would be nice for people to be able to farm atmas while leveling their other classes here so long as they have a Zenith(Atma/Animus) weapon in their inventory.