I'm no fan of the live action Transformers movies, but I wouldn't pin the blame on Michael Bay entirely. When it comes to the story that's largely Roberto Orci and Alex Kurtzman. Orci & Kurtzman are the screen-writing duo who wrote President Abraham Lincoln and a plot by the Confederates into The Legend of Zorro -- a movie which takes place in 1850.
I read the leaked script for the first Transformers live action movie when it hit the Internet -- Michael Bay actually cut out quite a bit that Orci & Kurtzman had in story at the time. Much of the excised stuff was a subplot featuring a CIA-type group and some civilian hackers that didn't add anything to the plot.