The main difference between the two is that the center cockpit allows for an aft cabin, while an aft cockpit allows for (generally) more interior saloon room. Though, note that center cockpits are usually for 40' and up...I have never seen an center cockpit that was below that.
I own a CAL 30 (aft cockpit) and have sailed from Honolulu to Cali on a CAL/Vader 49 (center cockpit). From personal experiance, the center cockpit allows for more deck storage as well (wind generator, solar panels, outboard/tender, etc.
I'm sure I'm missing a million things, but thats the basics, I believe.