Once upon a time, I posted a discussion of ship motions from the standpoint of a former naval architect. It's probably too much information, but here's the link to that discussion:
http://disboards.com/showpost.php?p=47077663&postcount=6
The bottom line is that there will be an increase in ship motion the further you get from midship. However ... (this is the YMMV part) ... what YOU feel on YOUR cruise has more to do with the sea state that you encounter (wave height, frequency, wave direction relative to ship heading, ship speed) and your personal tolerance for motion.
Most of the time the ship will operate without ship motion problems and you'd be fine no matter where your stateroom is located. But, sometimes, the waves just can't be avoided and a stateroom that is far from midship will experience larger motions than the staterooms closer to midship. Since you can't predict the weather that you'll encounter ahead of time, I wouldn't change stateroom location unless you already know that you are very sensitive to ship motions. Most people will be just fine in the aft staterooms, most of the time.
This probably should be a separate discussion, but the thing that bothers me in an aft cabin, far more than ship motions, is propeller vibration. Propellers are like the wheels on your car in that they need to be balanced carefully or they will cause vibrations. These vibrations are obviously most noticeable far aft ... i.e., closest to the propellers. Although ship operators go to great lengths to balance the propellers, it is inevitable that either marine fouling or perhaps some small damage to a propeller blade will mess up that balance. Until they get a chance to correct the problem, the result is a vertical vibration which is at a higher frequency than seaway induced motion, is relatively constant (for a constant ship speed) and is present even in calm waters.