I thought along these lines as well. Megatron is Missing in action as he warps around the universe randomly, and if we assume that Starscream was second in command of the deceps(although there has been no proof that I can think of to assume the Deceps have an assisstant despot), then the two leaders are MIA. Shockwave, having access to Cybertron could hide from the Autobots and use the communications there to contact and co-ordinate the Decepticons and become the stand-in leader. Then when Megatron shows up again, Shockwave either let Mes run the show or sits there and and explains that he has managed to do what Megatron couldn't.
Since I think its safe to say that the Starscream clones are officially Decepticons now (since they dumped Stars at end of Bridge too Close), we have gone back to one group of Bad guys, so we could end up with Shockwave's Decepticons and Megatrons "Elite" Decepticons as well...