I think this is a bug, so here we go:

Thread Title:
Ninjutsu damages are not matching the damages for weaponskills at the same potency (not using venoms)

Date & Time:
Around 20November2015 (took a long time to test)

Frequency:
Unknown, but presumed Always (Damage formula I assume is consistent)

World:
Balmung

Character Name:
Aria Placida

Monster Name:
Striking Dummy (various, including level 50 and 60 dummies)

Class/Level:
NIN 60

Party or Solo:
Solo

Steps:
I was testing Ninjutsu damage against Weaponskill and Ability damage to see if they were consistent. All tests were conducted against striking dummies in a housing ward, solo, with no buffs at all (any buff could have distorted the numbers).

I originally tested Mug against Hyoton. Both abilities show 140 Potency in their descriptions. Hyoton, however, consistently did about 3 less damage than Mug, as tested by finding their minimum and maximum damages. I then tested Aeolian Edge against Katon and Suiton, all 180 potency. Katon and Suiton appear consistent to each other, but were about 2 damage below Aeolian. Aeolian also allowed me to test against Fuma Shuriken, whose damage ranges matched. The final test was Mutilate's dot damage against Doton, which also matched each other. Damage ranges and combat stats follow.

Code:
Skill    Potency  Min Dam  Max Dam  Notes
Aeolian  240      1046     1157     Combo, Flank position
Fuma Sh. 240      1046     1157
Aeolian  180      784      867      No Combo, Rear position
Katon    180      782      865
Suiton   180      782      864
Mug      140      610      674
Hyoton   140      607      670
Mutilate 30       135      150
Doton    30       135      150
Code:
Weapon Damage:   74
Attack Power:    999
Determination:   479
Skill Speed:     651
Note that Katon and Suiton show different Max Damages. After seeing the 782 Min Damage on Suiton that matches the one for Katon, I stopped testing Suiton, because three values a minute is really slow testing.