It's worth noting that the Big Bad goes by 'the Doctor' before being outed as Cobra Commander.
Storm Shadow puts his swords together into a double-sided staff thing when fighting Snake Eyes at the end. Snake Eyes is played by Ray Park, who did Darth Maul, who was armed with a double-sided lightsabre staff.
Several years later, Channing Tatum said that he wanted to pull out of the film, but was locked into a three picture contract and would have been sued if he tried to break the deal.
Old Shame: For Sienna Miller, at least. Given only three cast members out of a large ensemble returned for the sequel, it's a safe bet she's not alone in this.
Channing Tatum hates the movie as well, and says the only reason he did it is because he would have been sued for breach of contract if he'd refused. (though Tatum admits he picked G.I. Joe because he was a fan of the franchise, which made him even more disappointed of the final product's quality)
Cobra Commander was given a new look because of the fact that Sommers thought that giving him a hood (or even a ski mask) would make viewers think KKK member when they saw him. Nor would they justify a form-fitting, featureless steel face-mask, since they wanted Joseph Gordon-Levitt's face to be at least partly visible.
Similarly, GI Joe becoming an international task force was done due to Paramount/Sommer wanting a high overseas box office pull for the film and thinking an all-US team of soldiers would not sell tickets outside North America.
Though, both of these plot elements (Cobra Commander's face-mask and GI Joe being an American military team) are brought back for the sequel, and the box office justified both decisions.
Race Lift: Ripcord is white in the original series. Breaker was a white southerner in the original Marvel comic run. Heavy Duty was still black but from Chicago, not London.
Stan Winston: The effects team behind the accelerator suits.
Throw It In!: Ripcord's helmet flashing holographic pictures of Scarlett. Originally, he was meant to be responding to the amount a virtual controls showing up in the HUD, but when it got to actually including the display in the visual effects department, they thought it'd be more amusing if it had her face popping up.
What Could Have Been: Rapper Common was offered the role of Heavy Duty's cousin Roadblock, but film screenwriter, Stuart Beattie, chose Heavy Duty instead.