I like the look of what is being planed.
In regards to Adv Jobs. I think once a specific rank in a class will be reached, you go do a quest to get an adv job trate or skill. Which will most likely be locked to the Root class. For example, PLD abilties can only be used as a GLA.
As for physical level. I like the idea that every 5 levels a trate is learnt the you have an option to equip.
Like, Rank 5, 2 trates, first boosts like STR, VIT, DEX and HP by 5%, the other does the magic side.
I know i will get flamed here, but they could throw in racal trates, Ryodin get like "large stature" which imterdated small mobs, The Lafdai can get small bonus. "Evasive", which is an evasion bonus based on the size of the mob fighting. larger the mob, higher the bonus.
This way they can keep your physcal level, and also gain from it trates to help boost you char.

/casts "Barfire" <me>