Well, any time you have a popularity poll and one of the choices is Cate Blanchett, the odds are stacked. That said, as sexy as she was with the short dark hair, I enjoyed the character of Mutt Williams even more. I've been around enough of those types of kids (and was one myself many years ago) to buy into the character.
Shia's right on the money with playing him as someone who doesn't have a great deal of respect for his elders\the establishment\whatever.
I also like the slight arc he goes through. He eventually cares enough to want to get the skull, help his mother, beat the Russians, etc. However, he doesn't completely lose his edginess. He doesn't go through a Disneyesque tough-kid-to-good-boy transformation.
By the end of the film, he hasn't completely made peace with his father leaving him and his mother. I thought his line "Why didn't you, dad?" was an excellent way to show that.