My 2 cents into GI Joe: The Movie.
If you don't like Lorenzo's approach to GI Joe, then you need to complain to Hasbro. Ryan smartly pointed out for Transformers, Hasbro has a say because it's
their franchise. Since it's in development stage, Joe fans seem to have a fair shot at changing the outcomes.
Though in my opinion... not having Cobra as a main villain
could work (hell, I'm shocked to even say that!). Check out the first arcs of GI Joe: America's Elite where the team dealt with a terrorist cell not entirely associated with Cobra. Of course it was a giant prelude to Cobra Commander's return to comics but this story worked.
I think they don't want Cobra Commander because he's stereotyped as a terrorist with cartoony plans like putting cruise missiles in fast food signs (Red Rockets!). Of course that wouldn't work for a movie! But that doesn't stop the filmmakers from putting him in realistic situations like in GI Joe: Reloaded.
As for the Duke & Alex team up, it's understandable. GI Joe is an American icon... but it won't play as well across the world unlike Transformers. Having an European hero like Action Man will help play in Europe. It's a business strategy but I don't think it'll hamper the movie.
All I ask is for a Snake Eyes & Scarlett romance subplot and I'm happy