According to Joseph Gordon-Levitt himself (via Collider), he’s not coming back for “G.I. Joe 2” as Cobra Commander. Why? Um, I don’t know, the reporter who asked him the question basically asked the question, and when JGL replied with a flat, firm, and unmistakably emphatic “NO”, just moved on to some “Dark Knight Rises” question that JGL just skirted by talking completely about something else. Wow. Celebrity puff interviews. Gotta love’em.
Jon Chu is directing “G.I. Joe 2”, and the only people we know are guaranteed back are Ray Park as Snake Eyes, Byung-hun Lee as Storm Shadow, and possibly Channing Tatum as Duke. Of course, JGL saying he won’t be back as Cobra Commander doesn’t necessarily mean Cobra Commander WON’T be back. “G.I. Joe” is essentially a fantasy/comic book franchise, and swapping actors isn’t too hard to do/accept. Just ask Edward Norton/Eric Bana/Mark Ruffalo.
JGL’s “No” comes at the 3:55 mark. You can pretty much skip the rest.