Ah! Serpentor!
Rarely can you find the exact moment when a series reaches its peak and begins its downward slope, but in the case of GI Joe, it's easy. The slippery slide to utter crap began with Serpentor.
Short story: Dr. Mindbender has a flash of genius. Cobra needs a new leader, someone who combines the qualities of the best leaders and conquerors throughout history. Cobra Commander, never one to think things through (remember when he tried to put his face on the moon?), authorizes the project that can only lead to his replacement if successful.
So the good doctor begins gathering the DNA from the greatest leaders and kings: Julius Caesar, Vlad Tepes, Napoleon, Attila the Hun, Ghengis Khan, etc. Hell, in the comic book they even put a little Storm Shadow in the pot for a while. Like a Bay Leaf, I guess.
Eventually they cook up this stuff into some sort of Uber-clone who becomes the new Cobra emperor. Of course, he was just as bad a leader as Cobra Commander ever was. And his outfit was at least three times as ludicrous. His management style consisted solely of belittling and insulting his employees and following all his edicts by yelling "This, I Command!"
But what really rankles about Serpentor was the fact that he signaled the shift from GI Joe being portrayed as a straight military comic/cartoon, towards a more sci/fi direction, completely ruining the premise. The storyline never recovered, never felt real or plausible again, and eventually led to its culmination (or abyss) in the GI Joe Movie, and the complete desolation that is Golobulous and Cobra-La.