Have you actually watched those old GI Joe cartoons as an adult? They are super cheesy now and actually kind of boring compared to the shows on today. I loved GI Joe and Transformers as a kid, but I have to admit that shows like Samauri Jack are superior in every way.
The GI Joe comic book, on the other hand, was some subversive stuff. Larry Hama worked in some dark stuff into that comic (Snake Eyes getting his face burned off by aviation fuel during what looked a lot like the aborted Iran hostage rescue attempt Operation Eagle Claw, Storm Shadow joining Cobra to find the assassin that killed his old ninja master) the that made it transcend the genre of toy-tie in comics.