Alot of good suggestions posted on this so far.

My favorites have to be changing the dungeons to give the normal mobs some more meaning EG:
1. Killing mobs mean more chests or more in the chests.
2. Killing the mobs weaken the boss so that it can be killed (faster/at all).
3. Killing the mobs open doors or remove barriers to allow progression through to deep parts of a dungeon.
These ideas sound interesting to me. I'm sure there are alot of variations that could be dreamed up by the SE team.

Having mobs drop gil, items, potions, gear, etc, etc could be a step in the right direction but it seems like there are more creative and dynamic ways of brining them into the fold.

At the end of the day it would be good to have SE focus not just on the reward at the end (Destination) but the journey of getting there. Making the whole experience enjoyable and fun rather than fun being relegated to "I got a new purple item, yay I got some fun today".