Yeah, it's a shame that he's marginalized during the second and third season. Cobra Commander is a straight up BOSS! The guy created Cobra from nothing, and built it to the point where world governments raised entire armies just to deal with him. It's a shame he's such a bumbling bafoon in the cartoons, as loveable as it is.
One of my favorite moments is actually this scene where he doesn't have his mask on, and he's eating. It's just this weird shot of the dude eating food, and it was fascinating. Sometimes the cartoon just has these moments were it's lucid, and someone makes a good call. They managed to humanize the character in like ten seconds flat, and make him all the more interesting. I like to think it was some lone, miserable, tired guy that was responsible for that. The crew hates him, they play pranks on him, they say his ideas are stupid... but every so often he has his way, and that's when there's a flash of competence or occasional brilliance.
It's the only explanation I can think of.
Oh, so what else do I love? The intro to G.I. Joe. That song, and three dudes throwing around Destro like he's a sack of potatoes.