After what was clearly meant to be Duke's Famous Last Words, the line "he's fallen into a coma" straight afterwards is obviously haphazardly added in. It also causes later scenes, such as a fight scene where Cobra-La specifically states that Duke died, quite narmy as well. Quite egregious is the Always with You ending where Falcon says to the stars "thanks, big brother", despite the fact that the characters have already been told that Duke was awake.
For many, the very idea that Big Bad Wannabe Cobra is now an evil ancient reptilian from the past.
Narm Charm: The musical intro where the Joes take out Cobra on Liberty Island from blowing up the Statue of Liberty where the over-the-top action, the ridiculousness of Cobra's attack, and the cheesiness of the song ("Crashing through the sky! Comes the fearful cry of...Cobraaaaa! (Cobraaaaaaaaa!) Cobraaaaaa! (Cobraaaaaaaaaaa!)") makes it looks like The War on Terror: The Musical. It's also beautifully animated, high tempo action, and a perfect distillation of the cartoon series in a single action sequence.
Signature Scene: The opening sequence. G.I. Joe foils a Cobra attack on the Statue of Liberty, with almost every single character who had ever appeared on the show contributing. Throw in Awesome Music and great moments like Duke punching Cobra Commander off the Statue.
The part of the vine trap sequence where Quick Kick, Snake Eyes, and Lady Jaye fall victim may or may not skirt the line between Fanservice and Fan Disservice.
Seinfeld Is Unfunny: Although this film was quite normal and even more serious at the time of its release, now it is at least So Bad, It's Good work with absurd doses of patriotism, an incredibly silly plot and every replica turning into mem.
Special Effect Failure: You can see and hear one scene where a H.A.V.O.C. Duke was on shoot beams instead of shells at an unseen target. Also the movie has other Joe vehicle's and Chuckle's handgun make actual gun noises, sometimes. A Mauler is seen behind and to the left of Hawk's Snowcat in the tunnel, but is not seen exiting, not that it should have fit anyway.