During a conversation with a co worker about brake sizes, he mentioned his was 12.75in diameter. He has a 350Z and back then they offered a 4 piston brembo package and the rotors being 12.75in. Thats not much bigger than non-sport model Q50's/G37's. If he has 4 piston brembo calipers for his rotors, do you think the Akebono 4 pistons will work on the 12.6 rotors? Could someone, theoretically, upgrade the calipers/pads now, then later on upgrade the rotors?

No, you will absolutely want to upgrade to the proper rotors. With smaller rotors you will have less pad being used which = less stopping power and possibly issues with error codes. If you are going to do it then do it right. Get the right rotors and pads. Replace the lines to SS lines while doing it. Replace all brake fluid to DOT4.