Have it be a set number of fates (even if its a huge amount, like 200 each) or add 'boss' fates for each zone similar to Odin and KB that drop the atmas.

Heck, even if its just PARTIAL mitigation of the problem, like have the drop rate go up with every fate completed that it didn't drop in, or letting us use alternate classes that aren't 50 so that we can at least get EXP for other jobs out of this.

This is literally a part of your character. Advancing your relic/zodiac weapon is pretty much the replacement for leveling up, and its going to keep building up on this base as the game grows. This is content you are required to complete to unlock weapon customization (once its released). This is like if they made it so when you killed a monster, there was only a 10% chance it would actually give you exp.