Im not a Joe fan, not one bit, yet Rise of Cobra is simply better. The plot, while silly, is more coherent. The action is interresting, unlike Transformers, where the robots looked like gray blurrs half the time. Fortunately they corrected that in the sequel.
The main difference between these films is that Rise of Cobra doesnt take itself very seriously. Its cheesy, hammy and its aware of it. Transformers had mood whiplash and could never quite decide if it wanted to be a kick-ass action film or a retarded immature comedy. It was dumb and obnoxious. I mean, seriously...masturbation jokes? Robo-testicles?
Another weak spot of transformers where the characters. Shia sucked, Megan was wooden and the robots barely talked (except Optimus, who was top-notch). I know giant CGI robots aren't exactly actors, but could they atleast have some dialogue. The average Decepticon line was "AAAHHRRRRRRRGGLLLLGGLLL!" Destro, Doctor, Baroness, Storm Shadow, Zartan where much more memorable because they where given some spotlight. Overall, GI Joe used the villains much more effectively.
I can't say for sure if Rise of Cobra is closer to its source material, but im going to take a guess and say it felt like a GI Joe movie. One last thing: Is it me or was this movie LESS patriotic than Transformers? Ironic for a toyline with the "Real American Hero" tagline.
I say watch GI Joe, bring some pop-corn and enjoy the cheese!