Yeah, I'm sure Michael Bay could call up some respected acting teacher/coach and say do you have anybody that is 21-25 that really has some talent. And the teacher would say yes, and then he would get their headshot and discover that she's a fairly average looking girl. Megan Fox is one of the hottest chicks in the world. It makes little sense in the movie reality that Shia breaks up with a 10 and starts dating a 6.
Also, you're probably overestimating just how good an actress you need for this role. It's not as if Megan Fox was being forced to bring a lot of dramatic weight to the character. It's basically a role where you're supposed to look hot, looked scared on occasion, and run around while things explode around you. It doesn't exactly require the next Meryl Streep or Julia Roberts to pull it off.
It's why the one girl from the first movie, Rachael Taylor, who played the Aussie CIA analyst turned down the chance to be in the sequel: http://moviesblog.mtv.com/2008/08/19/ra ... oud-of-it/
We're not talking about casting the Diary of Anne Frank by any means here. It's an eye candy role, and the fact that they've had to re-cast in the middle of production isn't going to make it less so. You have to remember what demographic the movie is marketed towards: 18-40 year old males.
And even if you do happen upon that 23-year old actress who is both beautiful and talented, I'm not sure she would jump at the chance to do the movie, even if she's an unknown. Any actress that wants to eventually be known for her acting ability and not her measurements isn't exactly going to be advised to jump into what is essentially an eye candy role. I wouldn't call it career suicide, but I don't think Transformers 3 is going to be the bridge to play Jackie Kennedy in some biopic 3 years down the road. It's more likely the bridge to play the hot chick in some raunchy R-rated comedy.
Doing a big Hollywood blockbuster your first time out isn't the most common path to staying power and long-term success. Just ask Megan Fox.