What we know at this point about Cobra Commander is that he IS in the film, but in an 'Emperor Palpatine'-type role. What exactly that will entail is not yet known. In terms of casting, I think it's important that they cast someone who can not only portray the character physically, but also provide the voice. Two people that I think fit this criteria are Liam Neeson and Alan Rickman. Although they don't have especially deep or raspy voices, it would not be hard to alter their voices to fit the snake-like vocals of the Cobra Commander that we Joe fans know and love. Hugo Weaving would also be a great choice, but that might draw unfavorable comparisons with the voice work he did for Megatron (which some people weren't happy with).