Concept Art World » Transformers: Dark of the Moon Concept Art by Wesley Burt joshnizzi.com I'm gonna speculate one of the reasons why the Autobots lost the war. The Autobots relied on a battleship philosophy for their ships. The Ark would have certainly made scrap metal of Decepticon motherships. But the Decepticons have the benefit of projected air power using fighters in conjunction with motherships. Decepticon Motherships we've seen are armed missile ships as well. As we've seen the Ark didn't have a fighter escort as it raced out of Cybertron. According to Hasbro's Transformer glossary entry the Ark was designed to launch protoforms to nearby planets. Meteor forms aren't fighters. But they can serve for orbital strikes as seen with the Decepticon attack on the US carrier fleet. The Autobots were at a strategic disadvantage using battleship doctrine while the Decepticons used aircraft carrier strategy.
That actually explains a lot. That and the fact that the Autobots only had one Optimus Prime; take Optimus out of the equation, and the Decepticons are universally more powerful, as well as more numerous.