I read somewhere that the producer wants a Ninja only story for 3, i can't see how that would be a GI Joe film, a GI Joe spin-off may be.
I think they need to go back to basics, better if its a reboot, but not a neccessity if done right. Have CC as a background character pulling the strings of no more than 2 major Cobra characters, with the rest being made up from mere troopers or Vipers. Similarly with the Joes being kept to 4 or 5 characters. Then have a much tighter story involving a hostage drama such as in Alistair MacLean's Hostage Tower were an international terrorist siezed the Eifel Tower. By making it more compact it would also free up the budget for employing proper actors not just those percieved as action movie stars.