Depends on how he is portrayed. I'd like it all to be as realistic as possible. Keeping that in mind, there are 2 things Cobra Commander must have for him to be recognizable:
a) Something covering his face
a) Cobra sigil (even if its an early version)
I can live without blue as Cobra's trademark color. I'd go for black.
Perhaps, for the first film, he could be sporting a "proto-costume", like this:
As for Destro and the whole "cobra commander working in the shadows ala Star Wars' emperor" rumor-thing...
if I were in charge of the whole thing, I'd have Destro be a sort of "Ra's Al Ghul" (Batman Begins' interpretation of the character). That is: He finds in Cobra Commander (who isn't called that way yet) the suitable "apprentice"/tool to achieve his "long term global master plan", like with Bruce Wayne.
Think of Hitler for a moment. He came out of nowhere. Slowly, through baby steps, he started to catch people's attention. He was a natural leader. A great orator. The "powers that be" found in him just what they needed. So they financed him.
So. Think of Destro as the main foe. He is the one the Joe team are after. At the same time, Destro (whose real identity isn't known at first, like with Ra's), starts to finance a new organization, "Cobra", under the leadership of Cobra Commander (who adopts this title).
What ends up happening is that the "apprentice" gets out of control, just like with Hitler and Bruce Wayne. Hitler was more than "The powers that be" bargained for. And Bruce Wayne doesn't go for Ra's ultimate goal and becomes a vigilante on his own as Batman. He learned all his tricks from Ra's, but he fights and stands for other ideals in the end.
And Cobra Commander? Well, he would end up getting out of Destro's grasp. In the end, he would no longer take Destro's orders and it would start to work the other way around. This will be the reason for their troubled relationship, which could certainly end bad by the third movie.
I really hope they go this route.
