Ninja Force isn't a bad idea per ce, after all GI Joe is all about specifically trained teams doing specific missions. A team of Ninjas would make sense, as would a team of hackers or saboteurs. People trained in arctic conditions and people trained in jungle fighting. Arguably, given that it only lasted for half a dozen or so issues,it didn't outstay it's welcome but it did come at the time when ninjas were everywhere, making it look like a crass cash-in, and the way it was marketed lent strength to that argument.
The toys made a small mis-step in that era too - no holes in the back for backpacks. I suspect it was to make room for the ninja mechanism (the slash-y arms or kick-y legs and so forth) but it did annoy me as a nipper that it restricted playability.