Thanks for the suggestion, but I have a few concerns/questions for you.
If you change physical level into job level does that mean that your stats (STR/VIT/DEX/...) are going to be determined by your Job level? What happens if I change jobs? These physical stats become increased/decreased according to my other job levels?
-my problem with this is that there isn't going to be enough Job-specific abilities to learn to take me from 1-50 in a Job AND in a Weapon Class (unless you want to throw a ton of abilities/spells onto jobs and leave weapons closer to what they were in FFXI just learning some TP attacks). You need physical development to take quite a long time so as to have a nice stat progression. If you are going to remove physical levels I personally think it would be better to then have your physical stats be determined by your Weapon Class rank since it already goes from 1-50. But, then you get a problem like having a maxed out DRK change weapons from r50 LNC to r30 MRD and have all his stats reduced because of this just because he changed his weapon class. I think this puts too much limitations on people.
Also, you're saying that the skills/weapons you equip will determine your job. So for example, if I equip a sword, shield, and some abilities like rampart, heal, protect, etc. The game determines (FOR ME?) that I am a paladin?
-This is way more restrictive than what I am suggesting. In my proposal I choose to be a paladin (this gives me some specific traits/abilities) and then I pick from the weapon skills that I've learned what (non-class-specific) abilities I want to use with my paladin. With the extended favoring system I'm talking about, certain "paladin builds" are going to be way more effective than others, but this system doesn't constrain you as much as what I think you are suggesting, it allows you to go against the grain or more specifically adapt to a very specific situation.