I think physical level was supposed to serve the purpose of specializing your charachter, but they probably gave too much freedom.
rework how stat works, decrease or eliminate diminishing returns from stats, however.
Physical levels should have base stats maybe slightly different for each race, maybe not. for example
lvl 10 highlander

base stats

str 20
vit 22
dex 18
mind 18
int 17
pie 21

at 50

str 90
vit 98
dex 86
mind 82
int 84
pie 90

*the stats here are arbitrary, im just using them for example, they could also be overall lower, once again just an example.
now there would be some status points you could freely alot, so as to customize your charachter, say you have 20 to 30 skill points you could a lot freely. Id say you can completely reset your freely alotted points once per leve reset. the idea is, this is your base charachter growth, this is who you are, I'd make it permanent but i dont think most people would get behind that.

far as the armory system, i dont think anything is wrong with it at all, some skills may need to be exclusive, or have how well they work on sub reduced, but overall thats already in place, buffs buff for less, take longer to recast, cures are about half as effective but still cost the same on DoW, same with magic,
for class uniquness, i think most native weaponskills should have unique animations, by animation i mean how the charachters move, not just the special effect. The job system will further add uniquness with special traits, and skills, the also should continue to have certain discipline specific skills learned via quests, and guild marks.