I imagined it like all the skills have some variables assigned and crafting adds or replaces some of them.
For example, Crippling Blow: Melee, Weapon damage, Crippled, AoE. Fossil Strike: Ranged, AoE, Slow, Oil, Earth Damage. You combine these skills and get a Crippling Fossil Blow skill which converts all the damage to Earth, slows and have a bit wider AoE with your Melee weapon. Crippling Blow + Heart of Steel restores your physical armour and have increased damage to the enemy physical armour and so on.
It seems that I was wrong. At least we will have some more skills.
