G.I. Joe: The Rise of Cobra/WMG

Storm Shadow returns!
Okay, maybe not a WMG per se; you can't really kill him off after just one installment. But! After being stabbed and falling into the icy arctic waters, Storm Shadow floats down, his bodily functions slowing as he descends into hypothermia. Of course, he's Arashikage. So he uses the Sleeping Phoenix to temporarily suspend his life, allowing him to continue to exist as the explosion of the underwater base throws him onto the ice-sheet. He is found by Cobra Commander, who isn't one to waste resources, and revived along with a good dose of mind-controlling nanobots. Storm Shadow then shows up in the sequel, brainwashed but with a Heel Face Turn totally possible.
 * This one might actually have some legs to it. Remember Rex's demonstration of the healing nanomites? It's quite likely that other troops, like Storm Shadow, got them as well. And look at his final fight with Snake-Eyes. He's sliced up to hell and back, but look at the cuts. Not one of them is actually bleeding. By all rights, he should've been covered in the red stuff.
 * Or, y'know, Bloodless Carnage.
 * In the DVD commentary Sommers spends about five minutes all-but-stating that Storm Shadow would be back in a sequel, pointing out numerous ways in which he could survive.
 * Confirmed. The part about him returning anyways.

The Baroness didn't fight off the Nanomites.
They're still inside her and working absolutely perfectly. Cobra Commander is just using her as another The Mole, so she can free him and Destro in time for the next movie.
 * Alternatively, she was never brainwashed in the first place. That was just a lie to make it easier for Duke to believe it. She knew all along that  was really The Doctor. Her High Heel Face Turn was just part of his Evil Plan. In the sequel, the "reformed" Baroness will cut some kind of public deal with the President of the United States   in order to allow her to get close enough to The Commander and Destro in order to free them, echoing Destro's plot from the beginning of the movie.
 * You just unraped my childhood and made The Baroness badass again. God bless you *sniff*
 * You're welcome.

Storm Shadow didn't kill the master.
Despite the change in age and having a sword rather than an arrow, the story is verbatim to the comics: Hard Master is found killed by Storm Shadow's weapon and Stormy runs away, everybody believes Stormy did it due to his jealously of Snake-Eyes.

Cobra Commander is Tom Hansen
Tom Hansen meets Autumn, but it ends up badly. So bad, in fact, that it started his descent into darkness.

The upcoming sequel will contain "Renegades" in it's title.
G.I. Joe: Renegades is being put on hiatus due to possible brand confusion with the movie's sequel. If the sequel is called, say, "Renegades of Cobra", unaware viewers might think its in the same continuity as the cartoon, which it isn't. Having two continuities use the same word? Can't have that.
 * Given that by the end of the movie, maybe it'll involve the President pardoning Cobra and then having the Joes implicated as terrorists, leading to a Clear My Name situation for the Joes.
 * Jossed. The title's since been confirmed as "G.I. Joe: Retaliation". However, given the above bullet point still in play, the plot could still have elements of Renegades in it.
 * Another addition to this is the newest trailer, where the "President" implicates our heroes as traitors