We all want movies to be the best they can possibly be. However, having personally read more than 3,000+ pages of G.I. Joe comic books, AND having watched every episode of the cartoon series, I can say that this film WAS a legit Joe film. Yes, there were several issues and deviations from comic book canon; however, it DID have multiple elements that certainly gave it the correct "feel".
Since 1982, G.I. Joe has NEVER been 100% serious, and for the most part has ALWAYS been over-the-top and slightly goofy (I still love the hell out of the series despite this...). They have fought ninjas, robots, cyborgs, terrorists, mutants, and even teamed up with the Transformers several times. It is what it is, and this was along those same lines. If I was 25-30 years younger and saw this movie, I would have greatly enjoyed it. As it stands, I enjoyed it for what it is (which is NOT best picture, but is a G.I. Joe film that significantly improves on the first movie/mess).
I DO suggest that if at some point a movie were to be made that was a bit better, they would need to re-boot and follow the DECLASSIFIED mini-series, which is superb Joe story-telling at its finest.
(suggested reading: Snake Eyes: DECLASSIFIED issues #1-6; Marvel's G.I. Joe issue #155).