The % weapon damage for spells only serves to compare weapons and spells between them. Meaning, that you get the idea of the damage you would deal with 1 staff or other, or with 1 spell or other, judging by the experience you have.
We cannot compare mage's damage with rogue's nor warrior's. We do not know how is the formula exactly, how much intelligence, dexterity or strenght matter.
It is obvious that warrior weapons will have more weapon damage than staves, due to AAs, but we do not know how the damage from skills are calculated exactly. It is obviously not only weapon damage, there are other modifiers, and from the tweet of Mike Laidlaw, the formula is not easy to explain...