G.I. Joe/WMG

Transformers and G.I. Joe are both the same on-line game being played by hundreds of different people
Transformers is there due to it being part of the same continuity as G.I. Joe. When characters die, that means their accounts got suspended, or they quit. When, but comes back later, that means he lost his account for a while, but revived it. Also, that bum in "Only Human", who is actually is him after him losing his membership, but still being able to play.
 * However the fellow kid who plays as Cobra Commander must stink at the game.
 * And Starscream and Cobra Commander are the same person, just with different accounts.
 * Going by that logic, another kid plays both Hot Rod/Rodimus Prime and Serpentor.
 * I hope not!

G.I. Joe can't beat Cobra because Cobra can actually win in a war of attrition.
Let's face it: how many battles does Cobra win? How many battles do the Joes win? No matter how many times the Joes win, Cobra always have better manufacturing abilities and more troops. Sooner or later the Joes will either lose funding because they fail to achieve victory, or cross the Moral Event Horizon, being unable to continue fighting honorably against an enemy that refuses to die.

Cobra is a front for NERV and/or SEELE.
Think about it. The bizarre wheels-within-wheels plots? The cloning (in the comics) that brought dead characters back to life? The ancient DNA of military leaders of the past used to create Serpentor? The bizarre vehicles? And where do they get their money, anyhow?

Both NERV and Cobra have a leader figure who feels the need to hide his face constantly. Perhaps Gendo Ikari saw a little of himself in the shattered wreck of a man who would become Cobra Commander.

If that's not enough, take a look at the Red Banshee. Looks like an Eva Unit with wheels, doesn't it?

This dovetails nicely into the theory that NERV uses Cybertronian technology. The Red Banshee is a sapient transforming killing machine, and there have been many G.I. Joe/Transformers crossovers.

Cobra and G.I. Joe are working together to Defraud the American Government.
You never see Cobra Commander's face because he is an Ex-Joe. If his face was known, then The Plan would fall apart.

A long time ago, he went AWOL to form Cobra in partnership with Duke. Cobra Commander puts forward flashy, amazingly inept plans that look horribly dangerous but are unlikely to kill anybody. Duke saves the day, and the gullible President hands him money and a medal. Then Duke splits the money with Cobra Commander.

By the time we start watching, the G.I. Joe and Cobra organizations are a haven for skilled but bizarre operatives who don't want to wear a uniform or have any military discipline, but still get all the benefits of being veterans. Snake Eyes could never maintain his position in any other military group.

It also explains why retired pro wrestler Sergeant Slaughter was a prominent member of the Joe team. Where else would you find someone who could realistically fake fights without hurting anyone?

And it's no coincidence that Cobra Commander always escapes the Cardboard Prison he's locked in just as Duke's visiting. Duke comes to bust his buddy out of prison so they can perpetuate their gambit.

Whenever a Senator gets suspicious about how Joe and Cobra have been fighting for years without either side losing a troop, Cobra puts on a meaningless but spectacular attack, such as drawing the Commander's face on the moon with a laser or sending swarms of weather balloons that spray laughing gas over suburbia. This doesn't hurt anybody, but the press will panics, and any thought of disbanding G.I. Joe will be forgotten. If the Senator is particularly determined, then he may become one of the few Cobra victims who dies.

Cobra Commander's old code name was 'Used Cars Salesman.'

And both sides have a hell of a lot of fun!

Cobra is Starscream's side project.
Cobra Commander is Starscream's Pretender shell -- an improvement of the one the toy has.

Starscream is not the only Transformers character doing this. Soundwave is doing the same thing as Dr. Claw.
 * But the Transformers met Cobra Commander
 * The Pretender developed its own personality remnant from having Starscream inhabit it for so long and then went rogue. This is the being that the Transformers met.
 * Alternately, Starscream's ghost was possessing the shell for his own purposes.

Cobra Commander has a cousin we are also familiar with.
And his name is Walter Kovacs, AKA Rorschach.

There is a family resemblance - similar costumes, in some continuities; similar masks, for sure. Rorschach sounds like Cobra Commander pitched down an octave in the movie; in the comics, we get jagged-edged speech balloons.

Also, they are both lunatics - paranoid, schizophrenic, psychopathic, sexually repressed, suicidally stubborn, and exasperating to friend and foe alike. This brings up all SORTS of hilarious implications because of the tonal differences in the two series.
 * Bullshit. We all know who Cobra Commander is REALLY the embarrassing cousin of. High-pitched voice. Face deformity. Snake obsession. Megalomania. Wants to take over the world with a murderous terrorist group. Lord Voldemort. Come on.
 * Okay. But if Serpentor was the man pulling The Commander's strings, then who was the man behind Voldemort??

The upcoming movies takes place in the future of the original series.
After the anything-goes 1980s turned into the politically-correct 1990s, the Joe organization were hit hard: People demanded more female agents, a wider range of effect, and more minorities in the upper ranks. Forced to re-organize under pressure from the government, G.I. Joe became something almost completely different from their roots: The individualism was replaced with standard black to avoid accusations of unprofessional behavior, control was transferred from the US government to the United Nations, and all that made them great was lost. They were even forced to adopt one of the most forced backronyms ever.

Somewhere in the world, COBRA is gathered around a computer screen and laughing. Evilly.

The movie trailer is lying massively, and the Joes will not spend the entire movie as Powered Armor wearing boy scouts.
In the movie, after an initial action sequence, the Joe's nebbish accountant will destroy the accelerator suits, steal the prototype, and become Cobra Commander. This will force the Joes to rely on their own skills instead of flashy Transformersesque Powered Armor. It would make sense for Cobra Commander to be wearing Powered Armor -- he's done it often in several continuities. The Joes, not so much. For them, it just seems kinda silly. Although seeing Dennis Quaid with a jetpack would be hilarious.
 * Speaking of Dennis Quaid with a jetpack...
 * Er... partially true. The accelerator suits are used in one action scene.

Serpentor was missing one world leader to make him complete.
Namely Ozymandias.

Destro is a Time Lord.
This one should be obvious, at least.

By "Only Human", Cobra Commander/Old Snake is dying.
Not much to go for except for the fact that he starts coughing as the episode ends and he's basically lost all his status and power.

G.I. Joe will get an Ensemble Darkhorse page to complete the Hasbro tri-fecta.
MLP:FIM has one, Transformers has one, next would be...

G.I. Joe is an offshoot of S.H.I.E.L.D.
Whether Joe takes place before, during, or after S.H.I.E.L.D.'s time is completely up in the air, but I don't see why not. They even face a snake-themed organization that can be considered a sect of HYDRA that split off into its own organization.
 * Joseph Colton was a former S.H.I.E.L.D. agent.

Generation 1 G.I. Joe is a string of preposterous stories told by an old, traumatized soldier trying to entertain children.
The actual Joe/Cobra conflict was a horrific shadow war costing some men their lives and others their humanity. Cobra was a brutal terrorist organization on par with real world evil regimes and the Joes were elite men and women doing very dirty work in the name of their country (yes, we're talking about Snake Eyes waterboarding Dr. Mindbender while Scarlet takes notes). American citizens knew the war happened and that they 'won' but don't know the real way they went about it. Flash-foward to an old Joe being asked stories about the war by his grandchildren. He can't tell them what he really did, so he cooks up wild stories and colorful, utterly non-military characters to amuse them until they're old enough. That's why the franchise got Darker and Edgier over time: his audience is growing up and he can ease them into the more truthful elements of his career.

That's how you get a war where pro wrestlers and ninjas can fight with lasers and no one ever gets killed.