Well, who knows how much notice the writers had about Season 3 being the last season. It's possible that they were continuing to seed the series with future plot developments to be concluded later, only to be told well after those episodes had been written (and production for them thus underway) that the series would be final and that they had to wrap things up.Originally Posted by Ode to a Grasshopper
Many other writers have suffered similar fates in the past such as David Wise, Simon Furman, Bob Forward and Larry DiTillio, which is why the ending of G1 (both cartoon and comics) seems rushed as well as the latter half of Beast Wars Season 3. I suspect that this might have been the case - if so, I can forgive the writers for not being able to wrap up all loose ends.
They should stick Jhiaxus in as a cameo Decepticon (even if just a background character or if his name's just mentioned in passing) as a reference too all the times Hasbro's axed stories prematurely.