These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Even Better Sequel / Surprisingly Improved Sequel: Better actors, no cheap gimmicks, the costumes of Cobra Commander and Snake Eyes were impressive, the effects were really good, all around it made more of an effort to be a GI Joe movie this time around.
Fridge Logic: So COBRA has infiltrated the US government and used it to wipe out the Joes? Smart plan and all except...Why is the original president still alive? If he's dead, then the world will never know that Zartan was impersonating him because there's no original to discover and save!
Then again, if Zartan's discovered, who better to hold hostage than the Commander-in-Chief?
It's more shown than explained but Cobra requires the real President's (probably alive) retina scan to access the nuclear arsenal.
It's also shown that they're torturing him to get information such as the location of the prison Cobra Commander is being held.
An insane brilliant well-funded criminal mastermind with legions of loyal troops and hi-tech gadgets. Where else are you going to put him except the most secure, top-secret prison ever?
Still good to have one of the best bargaining chips in your corner.
Why was the entire Joe unit (which is supposed to be pretty damn big, very well funded and critical to America's defense (considering from the way the President well Zartan as President anyway, asks for them by name and the cabinet is depending on them) sitting around in the middle of the desert in Pakistan, in the middle of a war-zone for that matter, for one highly sensitive covert job that required one, maybe two, infiltration teams (and probably ex-filtration assistance)? Why didn't they have a base in America where the majority of the Joes were (considering they don't have a base in Egypt anymore and seem to be part of the American military now)? (By the way, why weren't they on high alert in the middle of a war-zone after stealing nukes from the country that they were still inside of?)
Why was Flint stupid enough to leave an American Military division flag on a prison in another country where America shouldn't be, where they were carrying out a covert op that America couldn't be known to be responsible for? And why didn't Flint get court-martialed for disobeying orders on a covert op, risking the lives of his fellow soldiers, and doing something that could get America into politically hot water?
Why would Zartan bother framing Storm Shadow for murder fifteen years (approx.?) prior?
He's Just Hiding: Any Joe not seen killed on screen during the big massacre who was a character in the original might be presumably still alive, out there somewhere. Candidates include Scarlett, Ripcord, Breaker, and pretty much anyone else still alive at the end of Rise that didn't make it to screen in Retaliation.
Hell, any Cobra killed on-screen thanks to their heavy use of nano-machines, which would be able to heal them.
And thanks to Storm Shadow being alive and well despite his fate in the first movie.
Even Duke's death on screen doesn't stop this reaction.
That said, the backdraft calmed down a little when it emerged that another part of the delay was to add more scenes with Character Development for Duke and Roadblock.
If you think the fans were pissed, imagine Hasbro. The toys had been on the shelves for about two weeks, with more set to ship soon after. They had to take a massive loss by rearranging the shipping schedule. More Avengers and Amazing Spider-Man toys had to be put out to fill up the allotted space on many shelves, and a combination of a product glut and a lack of new products led to a decline in profits in 2012.
Narm: RZA as the Blind Master. The awkward expositioning ruins what would have been some otherwise pretty cool scenes.
Cobra Commander as well. His extremely deep voice renders lines like "I want it ALL." and "We're kicking you out of the band, Destro." hilarious.
One-Scene Wonder: Walton Goggins as the Warden of Cobra Commander and Destro's prison, who utilizes every second of his screentime.
Screwed By The Film Studio: The film was postponed nine months on almost the exact week that the toys went out on the shelves, which (as explained above) in turn screwed up toy shelves for the rest of 2012.