Nova Prime's crew leaving 6 million years ago was supposed to be ancient, with only a handful of guys like Omega Supreme actually knowing them. At that time, the earliest stated date for the Autobot/Decepticon war was a few hundred thousand years ago. Then they established the war as having started 4 million years ago, which closes the gap considerably.
But now the war started 6 million years ago? All these guys who were around back then like Starscream and Prowl are relatively young, but Cyclonus, Tailgate, and the others from 6,000,005 years ago are unspeakably old, lost to the mists of time? That's really stretching things.