There's tons of speculation going around due to the director insinuating that he's focused on fixing the mistakes in Rise of Cobra.
ROC made a typical error that a lot of western films make... they try to be "neat and tidy" and over-explain things to the audience so that people don't have to wonder or speculate. Heck, this is the origin in western fiction of the monologue-prone villain who explains the entire plot of the story, at the end, so that the audience can be "educated".
So, ROC tried to tie the characters of Cobra Commander, the Baroness, and a member of the Joes together on a personal level. It was a dumb move, that instantly neutered the effectiveness of the villains by making them either dupes (Baroness) or overly explained (Cobra Commander, who is supposed to be mysterious and unknown.)
At the moment, fan speculation is that Retaliation will perform a retcon on who the real Cobra Commander has been all along, and that "Rex" in the first film was merely making a grab for power at the end by naming himself "Commander" and revealing the existence of an organization called Cobra. (Contrary to what it seems like, there's no indication in the first film that Rex is inventing Cobra on the spot. He's just playing the hand of a Cobra take-over of Destro's empire now that Destro has been used up.)
Ironically enough, this would go along with several story arcs in the Marvel Comics GI Joe series where several people made grabs for power to replace Cobra Commander.
Of course, the more lasting damage to a character is the Baroness... by not only making her the sister of a good guy, but dictating that her "evil" personality was the result of mind control now removed, they pretty much have no way to use her again without a contrived plot where she is somehow made evil again just because. And even if that happens there will be constant angst and wasted time by people trying to "save" her, restore her to normal, etc.
