As things stand now the FATE system is used for only two things, farming experience and farming seals. As such the population treats it as you would any exercise in farming, they find the most efficient route and leave the rest to rot.

There needs to be a second system integrated into FATEs that helps counter this. For example the more times a particular FATE is defeated the less of a reward it should provide. If there is an enemy force attacking near a town and a mass of adventurers beats them down to a pulp then the next time that enemy scrapes together enough of their forces to attack they aren't going to be at full strength and wouldn't provide as much of a reward. Conversely the more an enemy force assaults an area and crushes the allied forces the more powerful they would become and the more of a reward they would provide. This would promote a cycling through regions as FATEs gain and lose value.

Also there needs to be some sort of repercussion to having some FATEs fail. XI had its conquest system where if the beastmen were allowed to control a region there would be a loss of npc bought goods and teleports, what XIV needs is something similar to promote participation in FATEs that occur in regions where people may have no interest in fighting but enjoy services that they otherwise wouldn't want to lose. You could have teleports to a regions aetheryte increase in price or become inaccessible, reduced rewards from local leves or even an increase in the number and difficulty of surrounding enemies.

Heck you could even take things a step further and have a regions status effect special events FATEs. For example if a region is left untouched and the local beastmen tribe is allowed to gain strength you could have special bosses or even roaming primals or the empire could take advantage of the chaos in a region to launch a special operation. Conversely in a region locked under control you could have more festive events take place or the weakening of one enemy force providing opportunity for another force to move in.

You manage to engage players more in the FATE system as a whole, increase the variety of FATEs participated in and create a system of content that keeps players of all level ranges occupied when other content may run dry.