probably because as a condition of the tie-in license they were told 'don't introduce any new Cobras like
or whoever', don't introduce new Joes and don't do anything with
because we don't know what 2 is going to do.'
like how Lucas wouldn't allow any novels to deal with Luke and Leia finding out anything about their mum until after TPM.
which was why i wanted to do the Shads as villains in stories: new characters that would probably never appear in the films and who could be killed or maimed as stories dictated and not have to worry.