Ninja is very rare. Nobody really use them. They are outclassed whatever build you make.
High Wizards are better than Magic Ninja.
Assassin X are better than Melee Ninja.
Champions are better than KS Ninja.
They are trans classes while Ninjas are only extended classes so some would say this is expected.
How about comparing them based on usefulness vs extended classes.
Soul Linker are usable during WOE, MVP support, MVP Solo.
TKM's are good for leeching and is strong on chosen maps.
Gunslingers, though not too many, is viable on monster hunting, WOE, PVP.
I can't think of any use for ninjas.
I know adding/modifying skills can be hard to do but please consider increasing damage output.
They also have very few equips to choose from.