I think if were talking about what characters should appear it would have to be characters best suited for the story, rise of cobra was pretty much an introduction movie, several favorites were there but some characters were uncessary like snake eyes and shadow storm whose only involvement really was hired muscle and there own rivialry backstory. But nevermind there still pretty cool characters plus we have a different background to play with in the sequel along with the comander and destros past.
So to recap, Zartan is the president, Cobra Commander and Destro imprisioned, Baronness in re-hab and finally it lookes like Duke and Ripcord have become fully fledge Joes.
Essentially, with Zartan in discuise he is going to need someone who has the same kind of mind to help transform him back into his normal appearance. Then there is who would the cobra commander trust to continue his work whilst he is incarcated... For that we can only suggest Dr.Mindbender, who only had a brief cameo but i think Kevin O'Conner should reprise the role and make it a much bigger role at that.
secondly, i kind of imagin the joes are going to become outlaws as Zartan is in control and the goverment was in connections to the mars corporation so i could see the Joes going on the run, the only way they could move undetected across the world is if they were on a sub, to which i feel the character of Shipwreck should appear for that purpose.
Third character i would like to see is Tomax and Xamot, reason for this is that you can see what Cobras plan was a controlable obidiant army, possibly a clone army. Tomax and Xamot would suggest cloning expermients and having them in the movie would be great sideline for characters the Joes could fight.
finally the fourth character Firefly - with shadowstorm gone, we really need another rival for snake eyes. he would be a good fit. Plus he has good tracking skills.