Funny, I just got to thinking about this, and you know what? Maybe a fresh begining wouldn't be that bad. Start right back at ground zero. Intergrate what is going on in the world right now. Terrorism has large, well organized organizations and the Military forms an elite team to do something about it.

During the forming of this group, a shrewd dissadent (Who later becomes Cobra Commander) who has been using pyramid schemes, and maybe even a quasi-religious organization (think Scientology but used for early cobra recruitment). He begins an organization to make "the Perfect World" and goes from peaceful/political means to gathering guns for the future showdown with the evil agents of democracy. He runs across Destro in his gun dealing and gets introduced to the "Whos-Who" of terrorism (maybe even Osama Bin Laden) and manages to dissusade many of their disillusioned followers that HIS plan for the world is better.

Slowly he becomes more and more powerful much like Osama Bin Laden and his organization, until he IS the name and face (or faceless figure) behind global Terror! During the formation and workup phase of the new Task Force Echo (Code named "GI Joe"), they must shift gears between fighting little bands of poorly trained and organized terrorists and fighting a terrorist ARMY!

GI Joe's roster could be filled out by making billets like ;

Commander; Code name "Hawk": Currently held by Gen Clayton Abernathy
First Sergeant; Code name "Duke" Currently held by Conrad Hauser
Team Leader one; Code name "Stalker" Currently held by Lonzo Wilkinson

Then if a character dies, you can put a new person in the billet and they take that persons place. So it might be "Stalker" but it's no longer "Lonzo Wilkinson". This way Hasbro can still put out Quick-Kick, crankcase etc without having everyone saying "But they're dead!" And if they make the action figures "look" a little more generic, (think of old 1982 V1's) then if you have a character of someone who is long gone..."poof" Greenshirt replacement!

You could even have one of the Joes have a father or brother or uncle who is part of Cobra (think like the brother's Stall). Maybe one came from a poor rural community where Cobra convinced a lot of the people there the goverment is their enemy and Cobra is like the local Moose Lodge or Masonic Temple. Everyone is a card carrying and dues paying member thinking they are supporting lobbying in Washinton and the advancement of their own political veiws, when in reality the money is going to terrorism and attacks on civilian and military installations.

Entire towns and communities could be under cobra control and GI joe will have a hard time sorting out the "Hard Core Cadre" from the "conscripts". (Had to break out my communist manifesto books for THOSE terms!).

It could be the begining of a GREAT new world if they do it right and forget ninjas and clones!