This will probably get overlooked, but should be in every game:

Open PvP no restrictions (all servers)
NPCs should be attackable

Anyway, now that I've got that out there, something more within the scope of an FF MMO:

The best kind of PvP is party or raid PvP. Solo PvP is just plain silly, and shouldn't even be an option. What would be cool is if they did PvP events that would temporarily give you an advantage in PvE. Like perhaps a scenario where you have to fight to control an area, and the winning city gets +10% attack or something for a day or week.