From ROTF we get the impression the Decepticons were the older faction compared to the Autobots. Heck their founder the Fallen was still alive. While the Autobots entire history was written on the Allspark. But situation could be similar to Beast Wars and Animated. The elder Autobot generation kept the shadier part of their history from the young generation of Autobots. Specifically about a certain Prime going rogue and being the founder of the Decepticons. Thus the Autobots could be descendants of the followers of the Primes while the Decepticons were descendants of the followers of the Fallen.