-No Aetherytes in new area (everyone has to walk)
-Aggroing mobs above the level cap on the way to the city (so you have to travel in parties).
As a personal request, just some elements from FFXII:
Rare mobs->
Chain a species of mobs to spawn a rare mobs that has rare drops. Zoning resets the chain, not time
Guild (the hunting guild)->
Go on hunts for a particular mob that may have special spawning conditions (like in FFXII, this was usually weather, mob chaining, etc), do not make these appear in FATES, just roam in the wild
Meaningful weather->
Change the efficacy attacks in certain weather and make dangerous mobs (above the lvl cap) spawn in the weather (such as the elementals in thunderstorm, rain, sandstorm, blizzard, etc), also make rare mobs chain from these dangerous mobs
Bazaar->
Trade large quantities of seemingly useless items for a bazaar item, or even trade rare mob items for a good bazaar item (such as the Tournesol)
Map changes upon weather->
In 12, some maps such as giza plains, or the desserts around dalmasca changed the accessibility to certain parts of the map in weather (such a creating and blocking paths).

MORE IMPORTANTLY, NO AETHERYTES, so all of the above is nullified by teleporting...