IMO, each class needs to affect skills as such,
Knight
Sword/Axe/Blunt Mastery: Damage +10, Critical +5
Smash: Damage +50%
Final Hit/Wind Guard: Cool down -60 seconds
Leap Attack: Damage +100%
Wizard
Fire/Ice/Lightning Mastery: Damage +10%
Bolt Mastery: Damage +10%
Bolt Composition: Damage +15%
Meditation: Mana Regen +200%
Archer
Magnum Shot: Damage +50%
Magnum Shot (crossbow): Damage +150%
Arrow Revolver: Damage (per arrow) +10%
Crash Shot: Minimum damage +100%
Alchemist
Fire Mastery: Damage +5
Wind Mastery: Damage +200%
Water Mastery: Damage +15
Earth Mastery: Damage/health x1.2
Spark: Maximum Damage +25
I'm certain that each class will improve the effects of certain skills, these are my thoughts :3