Where to start, where to start?
First, no nanotechnology. It looks good on paper and in the cartoons but I would have it where Cobra attacks the Empire State Building and various other U.S. monuments/eyesores across the country stirring up 9/11 memories and setiments. The U.S. thinks it was Al-Qaeda or North Korea that plotted the attacks but later learn about Cobra being led by a mysterious man named Destro and his accomplice Cobra Commander. Who is this Cobra? General Hawk is called in from Washington to investigate and he assembles a team of some of the best operatives in the world: Duke, Scarlett, Gung-Ho, Roadblock, Flint, Shipwreck, Ripcord, and Wild Bill. We see the origin of Snake Eyes and Storm Shadow.
Second, no internationalizing the Joes or globalizing them. They are a team of the best U.S. operatives, agents, and guns-for-hire in the world. Make them like Stallone's Expendables, a unique, fighting team ala like "The Dirty Dozen" or "Inglorious Bastards", a group of people who've enlisted and volunteered to be a part of a shadow, rogue group, that Washington only calls upon when the going needs to get tough.
Third, no accelerator suits. Just good old-fashioned heavy weaponry and artillery is all that is needed.
Fourth, Destro wears his mask all through the movie. No explanation as to why or how he got that way. Cobra Commander starts out as Duke's friend but during a tour in Afghanistan, he is badly burnt in a roadside bomb explosion and believed to be dead. Feeling as though he was forgotten and left for dead, he vows vengeance on Duke and the U.S. donning something like this:
Fifth, it'd feel Michael Bay-sized with tons of action, explosions, and shooting but also a swordfight between Snake Eyes and Storm Shadow.
Sixth, some of the Joes do die ala like "Transformers" but the cause is great and their sacrifice doesn't go down in vain or unquestioned. One of these happens to be General Hawk, whom gives the mantle over to Duke.
Seventh, Cobra Commander, Destro, and Baroness live to fight another day.
