The way J_Man presents his idea could work and work well for a TV show to toys synergy, and the comic line that follows it.
I also liked the way Reloaded began -- but Duke as traitor kind of killed that particular universe.
The movie also will spawn its own separate comic universe, which is good.
None of these, however, are the main through-line of GI Joe. Up to now, this line has stretched from Marvel #1 through America's Elite #36, no matter how much some of us wish to ignore sections of that history. (Mine includes a lot of the Eco-Warriors and ninja Scarlett eras).
When IDW starts their through-line, their central GI Joe book, I hope that it will either be a reboot, or a new cast -- but really, a reboot. The reason being, after WWIII -- even if Cobra goes out with a whimper -- that world is really messed up. There needs to be a retribution against Cobra. MARS will be dismantled for their part in overthrowing the US and UK governments. The US and UK -have- been taken over, no matter how briefly. DDP has sent the Middle East into a hot war -- truly, everywhere is a hot war zone.
I'm just not sure what good GI Joe can do in a post-DDP-WWIII universe. They wouldn't be used against Cobra; they'd be used to rescue hostages from opposing countries. They might be called upon more for occupy and control, not in and out. This isn't a world where a counter-terrorist group can sweep in, complete a mission, and leave again; the areas are /too/ unstable.
The point of an ongoing comic, to me, is to maintain the status quo; it's the fundamental difference between a comic book and a movie. (Movies require resolution.) Take Batman: Batman fights the Joker. The Joker nearly wins, but Batman defeats him. Bats sends the Joker to Arkham. Later on, the Joker escapes, and the cycle begins again. You can still have character growth within this cycle, but the cycle is necessary. The cycle is what brings back people who have read for a while long ago; it gives readers a certain measure of what to expect. The cycle /can/ be modified; the Joker can win a battle: ie, maiming Barbara. Killing Jason. Ultimately, however, he must be caught and not killed -- not unless you have prepped a new Joker in the wings.
With GI Joe, its cycle must include a nemesis. I'll even be a little broad with that. That nemesis can be Cobra, the IGs, Headhunters, Red Shadows. GI Joe needs to foil the nemesis' plans, or at least, the nemesis' -overt- plans. The nemesis must be able to have a 'foot in the door' peskiness, but never be able truly to exploit that inroad. Once they do, once the nemesis gets -too much- power, then something lie the last two years of America's Elite /must/ follow. And, once you open the door all the way to a world-wide hot war, how do you close it again?
You'll note I didn't mention characters in the GI Joe cycle. While I adore Scarlett and Breaker and the rest of the original 13 like anyone else, this is the military. People get hurt, people die. That's why there's triple redundancy for every position.I seem to recall reading that the US Special Forces maintain this triple redundancy: One battalion is 'on alert', a second 'in training', and a third 'on leave' at all times. That way their operational battalion has had both prep and rest for the high stresses of the work their asked to do. The nice thing about cycling people in and out is, if a writer wants a particular character, that character can be pulled from leave or out of training to join the current ops squad. (Yeah, sorry Downtown. We like Short-Fuze better.

)