I was all with Serpentor, insane as he was. Lots of his troops were mesmerized by his badassedness, but a bunch of others felt safer under the leadership of Cobra Commander. There was even an episode about that. I don't remember the exact title but it was something like "Into Your Tent I Silently Creep."
But the Cobra-La shit went off the deep end. If Sunbow had continued the show, they either should have followed the movie, at which point Serpentor and Cobra-La are all dead, OR the aforementioned were near-dead and fighting a civil war with the healthy, surviving Cobras.
I vote for the former option. Let Cobra Commander mutate back into a semblance of a man, pulling strings in the background.