Instead of abolishing Physical Level, a new tool of implementing "Racial Traits" gained through physical level would be a great way to keep Physical Level while allowing attribute growth to shift over to classes like planned.
System Explanation:
Every Physical Level gained gives the player +1(PL01-15), +2(PL16-30), or +3(PL31-50) Racial Trait points (RT or RP, but not RTP). These can be spent on various racial traits, or retrieved at a rate of 1 trait/period that matches with resetting attribute points in the old system.
Some example traits:
Sea Wolf Expertise:
RP: 4
To Equip: 3 points
Effect: You lose 4 piety to gain 2 strength and 2 dexterity.
Race: Sea Wolf Roegayden
Sea Wolf Rampage:
RP: 10
To Equip: 5 points
Effect: When you regain HP through a spell cast on you, you gain a temporary attack bonus. (+5 attack for 10 seconds).
Duskwight Stealth:
RP: 10
To Equip: 5 points
Effect: You gain a small accuracy and attack bonus when your target is attacking a nearby ally. (+2 attack and +5 accuracy when behind a target currently targetting another party member.)
Hyur Pride:
RP:15
To Equip: 10 points
Effect: You gain a small amount of MP each time you successfully hit an enemy with a melee attack. (+1 MP each time you hit with an arm from MRD, GLD, LNC, or PGL)