In their coverage of the Jon M. Chu news, The Hollywood Reporter had this interesting bit of news:
Sources say Paramount may find itself recasting major roles. While Channing Tatum is expected to return as Duke, it is unclear if Joseph Gordon-Levitt, whose dance card has filled out considerably since breaking out in Inception, will return as one of the villains. Insiders say Sienna Miller is also unlikely to return, with her Baroness role being recast or perhaps divided into a couple of new characters.
Cobra Commander being recast isn't a huge deal - heck, changing the guy behind the mask has been a plot in both the comics and the cartoons, so there's no reason it shouldn't happen in real life, as well. And with the right wig and glasses, anybody can be the Baroness. Now, would you prefer to see her recast, or written out?