I've always had the idea of placing footprints on the world maps that indicate if a Hunt mark was around with the size of the footprint alerting the player of it's rank. I understand that wandering around aimlessly in search of an B, A, or S rank monster is the draw of hunts but it gets old after a while especially when they respawn in different areas and walk around.
Also, how about a random event or something similar to ATEs in FFIX where during a certain weather condition, time of day, etc. if you in that area, a certain NPC will spawn that will begin a smaller quest line. Nothing too crazy but it will kind of give the NPCs a bit more personality. There are a lot of NPCs that say random stuff when you stand next to them, I think it'd be cool to expand on that. Like there's a guy in Limsa getting held up by two women underneath one of the stairwells. What lead up to that? Or why is the construction guy ALWAYS hanging from a building?
With the mentions of multiple world shards, how about a portal or wormhole that appears in random spots for a certain period of time that players must enter that will teleport them to another shard? There, they must fight thier way through hordes of enemies (similar to a tower climb dungeon like DD or HoH) to ultimately close it and put a halt to whatever it is trying to make it through. This results in better rewards of course depending on what floor you end up on. Alternatively, they could choose not to close it and let whatever it is trying to make it's way through resulting in a FATE-like boss fight with a difficulty akin to the Ixion, Odin or Behemoth fights. This would make players more motivated to close it rather than have to deal with a somewhat difficult world-boss.