You've got to hand it to Stephen Sommers. His movies are rubbish, but he knows it... and he has nothing but contempt – contempt, I say! – for movie critics who don't get that. There's a brilliant list of quotes from the GI Joe director up at Movieline. Best of the bunch: "I make the kind of movies critics love to hate. They love dark and depressing movies."
I haven't watched GI Joe yet, but I can only assume that Sommers didn't draw on the old cartoons – or on Cracked's list of Cobra Commander Terror Plots That Might Actually Work – for plotline inspiration.