How about having:
-humanoid enemy models
-enemies that do more than just wander around
-zones that don't constrict you to a path
-attacking guards at outposts and gates
-enemy encampments
-villages within zones
-greatly varying geology within zones
-swimming
-flight (doubtful)
-replace the Auction House with a real auction system
-with this new auction system, any new armor/items (as well as current ones if you're new) will be unknown to us unless someone has it on auction and it meets our query specifications
-not having armor in a listed form accessible to everyone will lead to less people wearing the same things
-more armor so every job/level combination doesn't look the same
-expand on the merit point system, making it open to all levels giving you stats and abilities to earn to make your character unique
-abilities for all classes that can be dropped besides just mage spells
-rework the levels, having 1000 hp at lvl 60 is not Final Fantasy at all
-have a natural heal-over-time and mana-over-time stat
-completely rework the NM and rare item system, such as making rare items drop off of possibly anything based on the mob's type, level, and location
-make NM's spawn possible anywhere in the zone
-get rid of preset mining/logging/harvesting points, make them completely random in places where the elements that are needed exist
-a place that's always accessible where we can just beat the crap out of each other or some bots without penalty or reward
-evil people/nations; honestly, since we only fight monsters you have no one to look at the way you would look at Shin-ra, Sephiroth, Seifer, Edea, Sin, Rufus, etc. Goblins, Orcs, Quadav, Yagudo, Demons, and the Shadow Lord do not install the same feeling in me.
I want to XP on that band of Taru and Elvaan bandits who have an encampment/hide-out in the desert, not some random animal that's just wandering aimlessly in circles.