Michael Bay has said recently that Transformers: Revenge of the Fallen was crap and pretty much blamed it on the writer's strike. Here's a direct quote from the interview.
“We made some mistakes,” admits Bay. “The real fault with [Transformers 2] is that it ran into a mystical world. When I look back at it, that was crap. The writers’ strike was coming hard and fast. It was just terrible to do a movie where you’ve got to have a story in three weeks.”
“I was prepping a movie for months where I only had 14 pages of some idea of whatthe movie was,” Bay goes on. “It’s a BS way to make a movie, do you know what I’m saying?”

However, both Bay and LaBeouf promised that the franchise's third installment, Transformers: Dark of the Moon, would rejuvenate the series, a sentiment Bay stands by in the Empire interview when he discusses shooting the film in 3D. He claims he made the decision in part because Avatar director James Cameron asked him to save the technology.
"Cameron was like, 'Mike, directors like you have to do 3D or it is going to die,' " he says.
Rather than going the widely criticized route of 3D conversion, Bay enlisted Cameron's tech and team to help him add an extra dimension during filming, a move he thinks paid off.
"I love it when you see these things: 'The 3D event of the year!' You see it every movie," he says. "There was a recent movie where you go in and before it starts they put up a little plate: 'These scenes were not shot in 3D.' Are you kidding? I think our 3D works really well with the robots, the size, the girth, the weight of it ... it's spectacular."