The idea i have to help balance out class and weapon skills is this. Instead of your magic/stamina pool helping to boost damage in its related area just make it a resource that determines how often you can use abilities in that pool. You adjust class and weapon abilities (damage, heals, debuffs, buffs,...) to compensate for this change. This would help allow players to either go mostly magic or stamina or go hybrid and not gimp their damage/heals in any way. How much magic or stamina you have would simply determine how often you can use abilities in that pool.
You can then start going though damage attacks and getting them inline with each other. Generally speaking if you have a spamable ranged/melee attack as a class skill then the equivalent weapon skill should do the same damage (adjusting for any secondary effects either might have). So if say Vampires Bane does X amount of damage at VR12 then the equivalent from a bow (Poison Arrow) should also do X amount of damage (once the dot is done).
This method would also go a long way to balancing out the classes in the game so we could stop seeing, "Sorc and DKs only for dps" in trial recruitment broadcasts.