Bay does have a big influence on the script, though. Two of the three writers on this wreck wrote Star Trek, but they admit that they try to write the script that the director wants - and these guys seem to have a pretty good handle on what Michael Bay wants. Also, after the writers' strike, they had to write a script around the action setpieces that Bay had already started working on during the strike.

Shia's line before teleporting to Egypt probably matches what the writers thought there. They were basically paid to fill in the gaps between the scenes Michael Bay was going to film whether they were in the script or not.

The prequel comics from IDW did, in fact, have a scene where they hunt Decepticons in San Francisco. I seem to recall them actually making a kill on the Golden Gate bridge (although I've never been to SF, so maybe it's a different bridge). Hell, they even repeated the "kill the Decepticon in vehicle mode so we can save on effects" in that battle, despite being a *comic book*.

Then again, the movie designs translate horribly into the comics. But I'm sure the comic storylines (that aren't tied in to the movies) would work well on the big screen, if Michael Bay was kept the hell away from them.