In short the FATEs should be inside of story quests. I'm ok with it.
Something like speaking with a NPC, then the NPC show you the location of a FATE and give you a special item that you need to wear to get the wanted drop from the FATE (to make sure that you speak first with the NPC for the story).
Or a NPC at the location of the FATE you need to speak first before you can join the FATE (see garlean invasion events 2012). Should work similar like the level-sync requirement.
Or a FATE that start at a specific time in a specific zone and then jump to another zone the moment it got finished in the current zone (see Atomos event 2012)
