I think one of the best ways to balance weapons/armors would be to introduce new mobs to the game that put a limited (see we do not need another patch of sweeping reform)-- puts a limited emphasis on the weapons that are not as valuable currently. Then sprinkle these mobs in with the existing ones, not make all new levels that feature only the new mobs.
Some ex:
a healer that is weak vs guns.
A mob that has a forcefeild that is weak vs guns, then standard armor behind it weak vs swords.
A mob that does piercing damage. I.e. add a construct that does pierce damage.
Basically new mobs that encourage teamwork as well as increase the importance of under utilized equipment.
Also, the game would benefit from new mobs regardless.
Or you could even just make Tier 2 and 3 wolvers deal piercing damage like they are supposed to.