Yeah, I just recently picked myself up a set of the ninja gear purely for the visual aspect, but am left confused now that I see the buff set. The defenses are odd too, particularly given the impression it's supposed to be melee based gear.
I suppose you could say the Elite Commando stuff kind of took over what the ninja gear maybe should have been buff wise, and we did need MA specific gear so when the ninja enemies were conceived I guess it made sense. Granted I'm no expert on the combat side of things, but the buff set for the ninja gear seems poorly thought out.