You asked the question, well have I got an answer......I like what could have been...
I waited and waited for new episodes after GI Joe the Movie and after Transformers had their "Rebirth", but there were none.
BUT there appears to have been plans in the work for another season and perhaps even scripts were written. Some of these scripts might have been bought and used by DIC (since some of the DIC episodes were written by Sunbow writers). But most of the ideas and intentions for this unproduced last season of GI Joe never made to the screen.
G.I. Joe story editor Buzz Dixon had this to say in an 1987 article about the G.I. Joe cartoon:
What will happen to G.I. Joe and Cobra on television in 1987?
"Changes," Buzz Dixon said. "Expect Cobra to be dramatically restructured. It will not resemble the Cobra of before. There will be big changes with G.I.Joe. The Rawhides and Renegades will be introduced, and will play a big part. Another thing is that 1987 will premiere a whole new series of high-tech vehicles for both Joes and Cobra. They will reflect the big upwards shift in the nature of the G.I.Joe/Cobra conflict"
From G.I. Joe Yearbook # 3 March, 1987
I had the opportunity to ask Mr. Dixon more about this when I interviewed him for the UGIJCW:
Jodie: Were there ever any plans for a third season of G.I. Joe, with the characters from the movie?
Buzz: Mike Hill, who was on staff at the time, made a brilliant proposal to send the Joes off after a somewhat new foe called The Coil for the never made Sunbow season three (there was a DIC season three, but they never bothered to ask for any input from me or Flint or Steve and frankly, we were just as glad). As I recall, Mike's idea was that following the Movie, Cobra would be shattered as a world-wide organization. Under the guidance of Tomax and Xamot, a new organization called The Coil (much more criminal in nature than military) would be formed, picking and choosing among the best of the surviving Cobra units. Cobra-La was utterly wiped out, no survivors, except for Cobra Commander, who would be slithering about in the background for the first half of season three as some sinister character of shifting alliances, then be revealed in severely mutated form in the second half. He would be playing the Joes and The Coil against one another in an attempt to destroy both and rebuild Cobra.
Sunbow season three was never made. Hasbro had been funding G.I. Joe out of their own pocket; they got a ridiculous deal from DIC to take over the series and they pretty much let them. The story behind DIC is much too long to go into here; suffice it to say these guys may not have been 100% responsible for the destruction of the animation industry in the late eighties but they sure helped!