Another deleted scene that didn't make it past concept stage (from a panel at TFCon last year) - Ratchet being hunted down by a group of exile Decepticons instead of Humans, lead by Lockdown... with Epps being killed off as well.
The original concept for the Dinobots was to have them lost/buried on Earth as guardians of the Allspark, trapped since the dinosaur age.
There was also an early concept that had humans building a base that could transform into a giant robot intended to destroy all Transformers on Earth, to be called Galvatron. The concept of Galvatron obviously ended up being a little different, and the human element ended up being KSI.
They also mention the lack of comics after TF3 DOTM... spoiling the ending by coming out before the movie, so the studio put a stop to it after that.