Who wins? Which of these highly trained special units emerges triumphant?
…Hmmm… Shield are highly trained agents… but the Joe team are the best of the best soldiers.
The Joe team is roughly a 100 members… I have no clue how many Shield Agents there are.
Shield probably has a bit better standard equipment… but in terms of vehicles and armanent… the Joes have the advantage.
The Joes are experienced in assaulting flying air-fortresses as well…
If it’s a straight fight, the Joes hands down… if its a matter of one team trying to take out the other… Shield gets it.
…Oh and the Joe team has several Ninjas… Ninjas might just be the deciding factor.
Joes, because they have the coolest weapons and vehicles. 
Cobra B.A.T.S, man…if they’re prepared.
I dunno, I think SHIELD has the advantage as they basically have the knowledge of nearly every superhero’s secret ID and can use it as blackmail to recruit them into battle.
Oooooh…Elektra vs Snake-Eyes…oh, please, Marvel and Devil’s Due, get together!
Might be?
Pshaw!
Name one global conflict that hasn’t been decided by ninjas.
S.H.I.E.L.D. if superheroes like Captain America, Wolverine and Ms. Marvel can be allied into battle, Joes if not.
Please, this is SHIELD vs GI JOe… not SHIELD plus super buddies… The Joes are friends with the Transformers so… Joes win anyway.
I’m not so sure of a Joe victory. Let’s face it. They’re used to fighting Cobra. Not exactly the most challenging of opponents.
Also, S.H.I.E.L.D. has some in house supers. Spider Woman and that vibrational powered girl from the most recent Secret Wars spring to mind. I’m sure that there are others.
S.H.I.E.L.D. has their own B.A.T.S. in the form of the LMD androids. The difference is that the LMDs are far more sophisticated than their Cobra counterparts.
I’m not going to make a bet yet, but I just don’t want ya’ll selling S.H.I.E.L.D. short.
What era of SHIELD? What era of Joe?
60s? Joe had real guns, not fancy blasters. Face it, SHIELD isn’t going to walk through the wall of lead those doughboys are going to put out.
80s? Hm. RAH Joe still has real_istic_ things, and metric assloads of them. The Helicarrier goes down when a flight of X-30s hits it. More Joes, more guns, better teamwork, too. And face it, Duke beats Nick any day.
- Sigma 6. Tricky. Down to just a few members now, but with near-superhuman abilities. The best soldiers in the country. Versus a fully operational SHIELD, with superhuman partners. SHIELD’s never been tougher. Maybe the Joes could escape a manhunt, but they’re not going to take Nick down for a few years.
I’m convinced that Snake-Eyes, Flint and Roadblock could probably dismantle SHIELD single-(er, triple) handed. If they convince Zartan and Destro to join forces temporarily they are unstoppable.
G.I. Joe has a cool theme song and a rallying cry. S.H.I.E.L.D.… doesn’t.
Victory to the Joes.
If SHIELD manages to hit the main suspenders depot for G.I. Joe’s “generic infantry” guys, the battle could easily swing in Marvel’s favor. 
That pun was elaborate and oblique. I love it.
They don’ need no Cobras, if Lady J, Sgt. Slaughter, & GI Jane http://www.yojoe.com/filecard/06/gijane_fc.shtml are available.
Heck, that’s just what I do. To a fault. I can’t help it anymore. Not even if I tried.
Danke.
Say, in this scenario, what happens if the Joes start collecting DNA samples from Marvel heroes to try and create the ultimate super-soldier to fight SHIELD?
(Eh, they’d probably end up with a guy who had the wit and charm of Hawkeye, the strength and agility of Charles Xavier, the tactical genius of Bucky…)