Each set of weapons was created with different aspects.

Relics focus on Raw damage, Acc, Atk, Racc, Ratk, and each has a unique aftermath.
Relics have the highest base damage in all three of the sets.

Mythics focus on Job specific areas. Many of the aftermaths are simular.
Mythics have the lowest base damage of all three sets.

Empyreans focus on status modifiers. All of the aftermaths are the same.
Empyreans are in the middle base damage wise.

The problem now is that Mythic and Relic ws's have weak modifiers. The weapons bases are fine. The weapons aren't the part that would need any adjustment to even them out, it would be the ws modifiers.

Each set of weapons has a unique set of properties. Damage output isn't the only thing based on the weapons. Effects, Aftermaths, Added effects, etc also come into play.