I thought I read that the Apple SSD connector is some sort of custom mini-PCIe variant instead of mSATA. Still doesn't answer the question of why, though. Maybe it's .5mm smaller and that makes all the difference? Maybe the electrical characteristics are required to be different for some reason? Maybe they wanted to kill the third-party upgrade market, forcing you to pay their BTO markup?

I forgot that the 13" retina is a little bit of a different beast, and actually has enough room for a thin 2.5" drive in there where the SSD normally goes. Designing an adapter for the connectors would be a pisser, though.

http://www.ifixit.com/Teardown/MacBook+Pro+13-Inch+Retina+Display+Late+2012+Teardown/11225/1