At first there was some speculation that Sommers might not be brought back, as there had been some internet scuttlebutt "that there had been some tension between Sommers and the studio," but any problems between the two seems to have been resolved.
It is expected that Channing Tatum will return as Captain Duke Hauser in the sequel, which is presently in development at Paramount.
Plot wise, all that is known right now is that Rhett Reese and Paul Wernick (Zombieland) were tapped to write the sequel. Apparently, the studio is happy with the draft they turned in.
Sommers is likely going to produce with Lorenzo di Bonaventura. G.I. Joe: The Rise of Cobra pulled in more than $300 million worldwide last year.