The Great Upgrade, as referenced by Optimus Primal during the Battle for the Sparks, was the 'upgrade of Autobots to Maximals'. This would likely have also been the point at which certain Decepticons, such as Ravage, were turned into Predacons. It also appears that the decision to upgrade was to reduce energon consumption and wasn't forced on the Predacons by the Maximals. Megatron himself reflected with disdain on how much energon the Autobots and Decepticons wasted when he first enters the Ark. Transformers also appear to be more organic, as shown by Megatron's wish to be solely mechanical in Beast Machines.