Here is what I think is wrong with the ATMA system: ( Cause/Solution)

Problem: FATE's are attached to them, FATEs are okay for certain things, End game related things are not.
Solution: Use a long quest for EACH ATMA ( You can use the same NPC if you want to. After the quest is done go back the NPC show him the ATMA you got, and then you keep it as a quest reward. ( So 12 quests, complete them all to receive the Atma Weapon.

The second portion of the Zodiac Quest is fine as you always know you are "progressing" for every objective you do.