Apart from the weaknesses that have already been mentioned, I'm so annoyed that Bay still insists on focusing on the human characters and not the giant robots when given the chance. The worst example was when they went to rescue Prime on the ship. Also, he's Optimus Fucking Prime -- he doesn't need anyone coming to help him, not even Marky Mark.
The other thing was, and this has been mentioned, as a long time Transformers nerd, so much stuff felt out of character and did not represent the characters well. The most obvious being that Prime doesn't kill humans. Period. That's the kind of thing that has me worried about Bay having any part to do with TMNT -- he clearly does not know how to maintain crucial character pieces.
Also, if Prime had rocket feet, why didn't he use them to get away when he was being chased.. like ever? >.>
Oh, and why can't Bumblebee talk yet.. That whole point seemed irrelevant as soon as everyone knew Transformers existed.