You guys gotta understand the use of 'em goes into toy politics. The concept of CORE came about and while it wasn't exactly around in the 90s, it sure was when GI Joe relaunched. Take a look at TF and see which characters are made over and over again. I'm not much of a TF fan but man, where I come from, Starscream got blown away by Galvatron and yet, he keeps on coming back in jet form???

In a way, the use of the ninja have different reasons depending on comic or toy. Toy-wise, it's all about the core now. As for the marvel comic, that's the story Hama wanted to tell and he freely admits it. As for DD dealing with it all, all I can say is that they don't know what else to do.