Having gotten used to the form factor of the MacBook Air, the new MacBook Pro Retina (rMBP) really took a beating on my wrists the first couple of weeks. The difference is that the MacBook Air has a slanted edge that is almost flat with the surface. Compare that to the rMBP, where its edges are elevated to a point where your wrists can dig into them. Yes, I realize this “issue” is a first world problem.
I usually use my rMBP docked to a Thunderbolt Display but it only took me a week or so of non-docked usage to find a solution for my aching wrists: Grifiti Palm Pads. These pads easily adhere to your rMBP (or other computer) and provide considerable comfort immediately. They also leave no residue, always stay in place, and can easily be moved around-again and again-to your liking. I leave them on the rMBP at all times, including when it’s closed. Considering how cheap they are, they’re one of my favorite buys in some time. I highly recommend them.