I like most of the appeals, with a few oppositions...

-I think most gear should be more cosmetic than impacting on the PC's performance (save "invisible" gears which exist only to produce bonuses)
-Stat allocation is a nice feature, skills/spells should encourage every job to use all 6 stats, and the elemental affinities should make it viable to use elemental spells while using a martial job
-Physical level should apply as a form of "tutorial" to give the player their pool of malleable points
-Discipline rank should only exist to increase attack options (the gamut of attack types available) which only get a modifier for using the same weapon they are native to, not the rank of that discipline (I think the OP and I are on the same page here, but still a bit unsure)