This would explain a few things: A weakened Megatron could no longer fly so needed a land based vehicle. Starscream never had an army of seekers. Why the Deceticons needed to pilot flying assault craft rather than transform into flying assault craft. Why the Decepticon armies in ROTF and DOTM were never in the air.
It does point out another question I wondered about. How did Soundwave and Megatron get back to the US from Africa so easily/quickly.
I assumed it was a "Cosmic Rust" gun.
Q was one of the cars in the raids at the start of the movie I believe. Brains transformed into a laptop, (well we saw him transform from a laptop and say how he'd just downloaded a bunch of info).
Wheelie and Brains weren't Autobots, Wheelie called them political refugees or something. And seeing that they were allowed to live with Sam they obviously fell under the radar. Or NEST didn't want former Decepticons having access to their base (fair enough).
Jolt's missing too. Maybe Jolt and the twins left on some off planet mission in between films? If the twins had been included and killed in that scene with Ironhide it would've ruined it, turning it in to a joke.