Saw it, enjoyed it, (MUCH MUCH MUCH better than the first one) and here are my thoughts.
One of the main characters dies during the big attack... and supposedly that death led to reshoots and the movie being shelved for roughly a year after it's originally scheduled release date... so.... WHAT WAS the purpose of the delay then?
Cobra Commander's pretty badass in this, and FINALLY looks badass.
But Zartan... or at least the guy portraying the Zartan version of the president really shined in this. When he gets to cut loose as a villain it's some of the most enjoyable character moments in the movie.
The Cobra plot in this felt like a sufficiently Cobra-esque plot this time around. Reminded me of some of the plot from the awesome "Resolute" animated feature.
Storm Shadow's character arc in this takes some sudden turns, (which makes sense in context of the cartoon and various comics incarnations) but he's still pretty god damn badass. His battle with Snake Eyes was fantastic.
A minor gripe I have though is that GI JOE, in this movie, feels like a much smaller force this time around. And no answer is given for the sudden shift (outside of the actors from the first weren't returning). No answer for what happened to Scarlet, the Baroness, General Hawk, Heavy Duty, etc.
And is it too much to ask for a cameo by Sgt. Slaughter?

I know he's getting old, but for many kids his JOE persona was like the Grimlock of the GI JOE franchise... and practically symbolized the show for many (him doing live-action intros and commercial cuts, etc. for the cartoon also helped).
Just find it funny as hell that it's taken the dude who did the Justin Bieber concert movie and the Step-Up sequels to set the GI JOE film franchise on a better course than it was with Stephen Sommers. XD