So I did study my butt off for the MCAT... my practice tests were all around 36-38 but the one that counted was a 31S (8-11-12).
As for my GPA, I have a 4.0 (and I wasn't someone who studied a million hours a day, I simply studied some but just understood the material).
I therefor don't think that it's due to a lack of preparation.
I also don't think that it is more perfect than a GPA. A GPA, as has been stated in other posts, is relative and ranks students in a school. It has constant professors that for the most part have an A from one year equal and A from another. The MCAT also ranks students relative to their peers, but unlike professors, the questions change test to test and the standards change as well.
Amongst my friends and other pre-meds, I have one of the highest GPAs yet one of the lower MCATs... not to mention, there isn't a correlation between our GPAs and MCATs as should be predicted by our GPAs ( us coming from the same institution, with the same professors), and our MCATs.
Not to mention, a test that you can do well on without understanding the material (aka take a Kaplan course and learn to do standardized tests), is not the best way to weed people out.
I also have to comment on the post that spoke about justifying all answers on a MC test. I am one of these people; I do horridly on MC tests, but if you ask me face to face, I'll knock your socks off. From my MCAT I still remember one of the questions... it asked which of the following gene splices would be used as a control [for the aforementioned experiment] (and then listed the options). I thought that there were two correct answers, the positive control and the negative control. Had they asked me how to do the experiment and what controls to use in an essay type fashion, then this wouldn't have been a problem; that being said I had to guess between the two and therefore probably got it wrong.