In Beast Wars, there was no full-scale war. It was a conflict between a small group of Maximals and a small group of Predacons dubbed "the Beast Wars". In Prime, the full nature of the war has yet to be explained. We know that there are other groups of Autobots and Decepticons out fighting each other, probably on different planets similar to Team Prime. We have to assume that the Autobots and Decepticons still report to Optimus and Megatron, respectively, but the two armies are divided into small groups on separate campaigns. So, yeah. Weak argument there.