Reputation/Faction used to be really kool way back in the day before MMOs went super easy-mode. You didn't run repetitive actions ever day just to build up and otherwise pointless faction just so you could use one half decent item. Your actions, all of your actions, used to have a literal impact on the world around you. Whole towns would become violent in your presence, shop keepers would offer discounts to allies, and of course special quest would appear depending on your allegiance.

If Square wants to go all in and do a full on real faction system involving all thirteen city-states, I'm all for it. But none of this half asses your faction can only go up and the only result is a special vendor is open crap.