Was Rex's mutiny against McCullen simply the seizing of an opportunity, or had it been part of the plan all along? Rex already had a special nanomite solution prepared for McCullen, as well as his own sub already branded with the Cobra insignia. It's worth noting that, in the sequel, both Zartan and Storm Shadow, who were previously loyal to McCullen, serve Cobra Commander without explanation, and nobody seems to have a problem when Cobra Commander abandons Destro, implying that Rex had quietly secured the allegiance of McCullen's lieutenants, and had been planning to hijack his Take Over the World plan all along.
When Zartan destroys the mind control chip during his surgery, McCullen looks concerned for a moment, while the Doctor doesn't even blink. Was this just Zartan being savvy and the Doctor not caring, or a sign that Zartan is already loyal to the future Cobra Commander? Either way, guess who's Cobra Commander's Dragon in the sequel.
Cliché Storm: The film is chock-full of every action movie cliche most people have ever seen. If you want an explanation, look no further than Christopher Orr's review of the movie, in which he decides to just let it speak for itself by providing 40 of the lines that sum up the plot and all of the typical one-liners and plot points it has. It's really a shame though, considering it had some great actors who did the best they could with the material they were given. Then again, for fans of the movie, this could be exactly what they liked about it.
Once a U.S. soldier, Rex Lewis was apparently killed in a failed mission, but had survived, secretly joining James McCullen's MARS Industries to research advanced nanotechnology, adopting the alias "The Doctor". Testing the mind-control application of this technology on his sister, Ana, the Doctor brainwashed her into aiding in his and McCullen's crimes for the next four years. Under McCullen, the Doctor developed the Neo-Vipers, brainwashed super-soldiers meant to do his bidding, and whom he horrifyingly killed if they were captured. After aiding McCullen's plan to wipe out four heavily populated cities, the Doctor used Ana as a hostage to cover his escape from the G.I. Joes, attempting to kill the Joes and his own allies alike as he fled. Betraying McCullen and taking control of MARS (which he refashioned as Cobra), the Doctor forced him into servitude, dubbing McCullen "Destro" and taking the identity of Cobra Commander for himself.
Fashion-Victim Villain: Cobra Commander. After switching to the metal full-head helmet, suddenly his skinniness becomes more apparent and he looks like a bobblehead or lollipop. One of the few cases where Shoulders of Doom might help.
Arguable since the Doctor is such complete sleeze that he lacks the flair of a typical Magnificent Bastard. Destro is much closer to the traditional view of the trope, pulling off his schemes with all the flourish of a Bond villain.
Moral Event Horizon: The Doctor crosses it when it's revealed that he brainwashed his own sister (who, it should be mentioned, is in mourning because he allowed her to think that he was dead), and is ready to kill her to save himself and spite Duke. While he was already a sadistic Mad Scientist helping in a plot for world domination, this revelation puts him over the line from bad to pure evil.
Narm: Cobra Commander does a grand entrance... and is caught and put to jail few seconds later.
Most, if not all of the dialogue from the Doctor (no, notthat one) is incredibly hammy, but Joseph Gordon-Levitt makes every single bit of it work. The crowning moment has to be when he declares himself Cobra Commander. Could have been very ridiculous (especially with that look), but it manages to be a Moment of Awesome.
The Doctor: The time has come for the Cobra to rise up and reveal himself. You will call me... Commander!
The entire movie is blocked with cliché's, and is burdened with a fairly thin plot and an overabundance of special effects, but despite or even because of that, it's extremely entertaining.
Older Than They Think: The movie pulls ideas from several different toy lines, comic books, and animated series. Many of the details that fans complain about the movie "changing" are taken right from the source material ... just not an iteration of the source material the complainer is familiar with (e.g., you don't have to like the powered suits, but if you know the G.I. Joe: Sigma 6 line, you know the movie didn't make them up).
Likewise "International Heroes" was part of the Action Force theme, and even briefly adopted in the DiC series. GI Joe also worked for the United Nations in Sigma Six.
Doesn't help that they come off of as more of a Battle Couple than Scarlett and Snake-Eyes, the ORIGINAL pair of leading lady and badass ninja.
The novelization seems to add considerable mutual witty banter and, yes, flirtation and, it also offers Ho Yay for Snake Eyes and Storm Shadow, who seem to be matching Official Couple (sort-of) Duke and Ana/The Baroness flashback for flashback, meaningful look for meaningful look. (Bizarrely carries over to the Ninja Showdown kid's book.) Oddly out-of-place due to the gist of their past relationship being "We really, really don't like each other."
Romantic Plot Tumor: The Baroness and Duke is pretty central to the storyline, even if it feels unnecessary to the mythos. G.I. Joe, after all, has no small shortage of improbable relationships across every canon. Ripcord and Scarlet, however, seems to have drawn almost universal scorn.
Special Effects Failure: While a majority of the special visual effects were well done, a CGI cobra at the beginning of the film sticks out like a sore thumb.
They Wasted a Perfectly Good Character: Cover Girl in this movie is basically just General Hawk's assistant before Zartan kills her. Cover Girl in the source material is a former professional model who took up driving tanks for a living. Not even the G.I. Joe fans realized that the character was supposed to be Cover Girl. You know you've wasted a character when not even the people with knowledge of the source material knew who the character was supposed to be.
WTH, Casting Agency?: You'd never imagine Marlon Wayans and specially Joseph Gordon-Levitt in this movie. Surprisingly, Joseph Gordon-Levitt really pulls it off, and Marlon Wayans... is, well, Marlon Wayans, although even he tones down his fundamental Marlon Wayans-ness a bit.
Channing Tatum as the leader of the Joes? Seriously?
Snake Eyes' mask having embossed lips. The idea of a character who doesn't speak having embossed lips on his mask is just ridiculous. It also proved distracting to the audience.
Rex's "Cobra Commander" helmet. Whoever was in charge of costuming either had no idea what the Commander looked like besides "shiny helmet", or tried to somehow combine Rex's look before he revealed his true colors with the look commonly associated with CC. The result◊ was...interesting.