I think it's good to keep in mind that Hama's IDW GI Joe (A Real American Hero) run was, itself, essentially a continuation of the original Marvel run. (With some discrepancies, but it started with issue 155-1/2, so it's definitely meant to continue the story he started in Marvel) If whatever new publisher picks up the license does continue ARAH with Hama writing, it stands to reason he would leave some plot threads untied (haven't read the final issues myself due to issues with my local comic shop; I'm still hunting a couple of the final issues), no matter how unsatisfying it was.
On the other hand, unless any of the current or recent writers for Transformers move to the new publisher, there is no reason to continue those stories unless directed/requested by Hasbro. It sounds like the publisher most interested in Transformers has their own angle for the title, so that is another strike against any stories continuing.
Finally, Transformers reinventing itself semi-regularly has generally been good for the brand, creating new characters and directions to explore along the way. Attempts to reinvent GI Joe...well, seem to have been less successful. Of the two titles, GI Joe is more likely to continue under the old direction, while Transformers is much more likely to...change.