Personally I think the fate part of endgame content is silly. Fates are a brilliant idea to aid leveling, gain seals etc, but not for quests. I know the idea was to get high level characters back into low level areas, but it doesn't help low level characters to have a horde of zenith weilding 50's charge into the fate and wipe it out, and potentially be at that for hours.

For the Atma I would rather see chimera/hydra style encounter trials, one for each atma with a quest chain to get to it. Single person trials, or party of 4, or 8 or even a mix and even if they only have a % chance to drop the atma once you complete it. You still then feel like you are making some progress. Set the trials in the low areas forcing the 50's to travel out of the cities. It wouldn't take too much effort to recycle some previously used creatures/locations, beef up their hp and damage etc.
The atma quest is not hard, but its soul destroying for one simple reason, RNG from fates.