No one knows for sure, but most seem to have assumed that Megan Fox is off Transformers 3 for calling Michael Bay a Nazi and generally turning her nose up at the whole Transformers franchise. The Wrap however has a different theory and though it seems kind of hard to swallow, they claim she left because Michael Bay thinks she’s ugly.
According to their sources when she showed up on the set Michael Bay thought she was too “pale” and was “underweight” and looked to “unhealthy”. They say she was a size 0 when she came to work and Bay wanted her a little thicker, around a 2 or 4. Bay sent her off to work on her look, and when she came back he was still unhappy. That pissed Megan off and she quit.
In a way this fits since Fox has been known to complain in the press about Bay’s excessive tanning requirements. But she’s too thin? That doesn’t make much sense. Michael Bay has since hired a Victoria’s Secret model named Rosie Huntington-Whitley, and while she’s certainly not pale, she’s kind of a stick figure. Next to the Megan Fox we’ve seen on screen, she’s a skeleton. Fox has always been a physically fit, curvaceous babe while models are generally anorexically skinny. As you’d expect, Rosie’s rail thin in every picture you can find of her, almost to the point that it’s kind of gross. Firing Megan Fox because she’s too skinny and then hiring an overly skinny model to replace her doesn’t jive. It seems more likely that Bay and Fox simply don’t get along, and whatever the reason she’s gone, it’s unlikely that her appearance was the real problem.
Check out the pictures of Megan and Rosie side-by-side below, and you’ll see what I mean. Granted, Megan could be skinnier now but even if she is, at worst she’d be no skinnier than her replacement.
And here's a much more recent photo of Megan, taken just a few weeks ago by the photogs at Just Jared. Still doesn't look skinnier than Rosie to me:
