If thats the case the the fix is simply increasing the discrepancies between skills.
If the perception is Skill 1 Does "Damage" and Skill 2 does "Damage" then edit it so that people understand that Skill 1 actually does "Damage + Destroy Head Armor + Stun Monster" while Skill 2 actually does "Damage + Destroy Body Armor + Prevent TP gain." Don't hide the extra effects that all of the abilities have. And make it so those added abilities work best on their source Weapon.
also include Status and Added Effect triggers to the Damage Pop Ups. If someone gets poisoned have it pop "Poison" as a damage display on screen for them. If a skill stuns have it say that when it works.