The Illustrated Guide was the first time it was revealed Primus could transform. Prior to that, he was just a head (which looked astonishingly like Hot Rod's) in the center of Cybertron.
This pic shows a scene from TF #58 (?), when Grimlock, Bumblebee, and Jazz, all recently returned to the land of the living after the Autobots suffered a devastating defeat at the hands of a mystically superpowered Starscream, stumble upon Primus and his mysterious guardian while escaping from a death squad consisting of Bludgeon (best Pretender EVER), Strangelhold, and Octopunch.
Decepticons. . . uh, well, uh, to have conflict? I don't doubt Furman would've gone further in exploring such issues, but the series didn't last. There were three other epic story arcs beginning when the series ended that weren't addressed in the shorter-lived Generation 2 series a couple of years later (a mysterious other race of mechanoids that ate one of the Battlechargers and fought the Dinobots while claiming to be the original inhabitants of Cybertron; a strange mental bond between Ratchet and Megatron that formed when Ratchet tried to sacrifice himself by destroying Megatron in a space bridge explosion, but failed and the two were melted together into one hideous beast; and the effects of Nucleon, which granted great power to Grimlock and revived many other dead Transformers, but which was supposed to have a very dark side effect). Galvatron from a parallel timeline had also arrived in our present, and allied himself with the present-day Megatron, and their tale was cut short when Furman had to bring in Fort Max to deal with Galvatron an issue before the series ended so it wasn't such a huge hanging thread.
(Funny thing: Galvatron spent all of the Generation 2 series frozen somewhere in the Arctic as a result of this final battle, and for some reason Megatron never bothered to dig him out of the ice. But it never mentioned the fact that Ratchet could feel Meg's thoughts, either. Overall, not Furman's best writing.)
Stories Furman wrote in Transformers UK and in Transformers Generation 2 implied that there were thirteen original Transformers, but one (Liege Maximo) had been long forgotten. I suppose differences among these led to their creating two opposing armies?
Or the one detail from the TV show about the TF's origins I really liked: at one point, Cybertron was conquered by the Quintessons (who, in the comics, were Unicron's equivalent to the Transformers) and the enslavement of Cybertron led to the two different factions.