If they bring back Baroness, they will have to bring back Joseph Gordon-Levitt as the cobra commander - I gave that some thought. See any character that wears a mask can be played by a number of different actors. Especially if the movie is trying to bring the budget down. But what you got to remember is that in the first movie you were introduced to Rex Lewis - aka became Cobra Commander... But also brother of Baroness. In keeping with that whole storyline... if you bring back the baroness and she is what works on the side of Rex/Cobra Commander, you gonna need some form of back story... saying Rex just reactivated the nanomytes the were trying to get rid of by the end of the movie is a cheap storyline.
It would be better to explain the complex friendship Baroness and Cobra Commander had before they became who they became. Yes they were brother sister but say Rex was adopted by the baroness family of which she always looked as him as younger brother then many years later Rex saves the baroness's life and she owes him a debt. So when the first movie happened she was too distrait to cope with rex's death but now she knows he is alive. Whose side will she be on, Rex or the joes