Battle UI
The first Thing that I would like to suggest is that instead of the Battle UI being the bar we have now SE makes it similar FFXIII. I think that FFXIII really had a great user interface for the battle system

Here are the options I think should be displayed
-Attack (Auto Attack)
-Defend (Evade,Block,Counter a attack)
-Skills (Can pick as many skills as your Stamina allows, and they go into a queue)
-Item (use a item or food)

Bonuses to Skills
Similar to FFXI I think it would be pretty interesting if some bonuses are added to Abilities, for instance if I equip Dia I would gain +2 Magic Acc. And to encourage less cross equipping maybe the bonus can only be gained when used with the appropriate class. Basically this would mix traits with Abilities, but making the trait only obtainable by the appropriate class which would be a good bonus in my Opinion.

Changes to Behest
-A Rank Cap should be added to camps, players above the Cap should be able to Level Sync though to the max level allowed to not kill Behest areas in the future.
-A bonus if you do Behest in your Homecity should be given to promote players to do Behest in the regions.
-I think the Boss should look more Fearsome, a way to do this might be to make the Boss of behest Bigger than there regular Family, for instance the ladybugs can be double the size.

Crafting
-Battle Type changes should be added to Crafters to make it easier for decent content to be added for all Disciples. While Crafters would be able to fight they still shouldn't be able to equip Skills from the Disciple of Magic and War as a penalty. and of course they probably won't be the best at most roles.
-In addition this would require the adjustment of many prices to make it plusable.

Music
As many have said the music in this game gets very repetitive, I actually had a idea that could work. Which is make it like Classical music which is usually long, and has the same Music just in different Tunes. Like it getting more Dramatic or soft etc, or give every region of the map it own remix of the main theme.