I'd rather use M&M, Fate, Window, any number of things over the "Naruto System" Same with the "Bleach System" It feels kinda restrictive, because it is, it has all the right names for everything, but still locks you in with that d20 mindset of 'you can't do anything but what we lay out for you.
It has hundreds of things, but you still have to actually use one of those hundreds of things, nothing you can do about it.
I love WoT, i HATE the WoT system, same problem, uts d20 refluffed and tweaked to work with WoT, but it just lays out things like spells and feats and feels restrictive and closed in.
The only WoT game i played that was any good was, i believe, Window, also i think i played a decent starter with Fate. These things allow you more freedom, or at least you can try to get a little more freedom for the intricacies of games. Systems that aren't so restrictive or planned out are best for worlds they aren't specifically designed for.