Personally, when I heard that the director from the Mummy was doing it I started doubting. I liked the Mummy, but all the ones after the original just kept getting worse.
When it came out in theaters I waited for a bit, cleared my mind of all thoughts about any G.I. Joe, and took it for it's own story. With that, I thought that they did a good job with the story and the effects were pretty good.
I agree that adding a mouth to snake eyes was lame, but I'll live with it. I thought that the chase scene through Paris was really lame, especially with scarlet riding the mortorcycle.
I think that if they do sequels we will see Duke taking on the leadership role that we have known him to have in the past and General Hawk will probably become more of a background role, or just go away completely. This was called the rise of Cobra, so I like how they gave a background story for almost everybody and we could see how all of the major characters relate to each other (even if those aren't technically right when you look back on the cartoons) and how Cobra came to be. I think it may have some pretty good sequals as long as I keep thinking of it as it's own story completely separate from the cartoons.