Only melee skills and ranged skills has to do with wepon damage.
You could devide skills like this:
Spells
Attacks
Passive albilities
Auras
So:
Auras like fana, might, conc scale on ur wepon/gear damage
Melee attakcs, ranged attacks uses damage from wep and gear
Spells like tornado, firestorm, blizzard, fireball etc uses + skills and +% elemental damage.