Well, since I've owned both extremes (Dec. 05 and Oct. 06) I've put together a quick list, add if you want. PS. I also went from a Cooper to a Cooper S so some of them might be due to that too.

M12 lugs to M14
Felt glovebox turned into hard plastic
Low fuel red light went from 70 to 45 miles (chrono)
Plastic vent in the boot privacy guard was added
Shift boot is lower on the shift lever
Fitment of rubber seal on the bottom of the rear window is MUCH better
There seems to be a lot more torque

Wait, the last one is due to the added supercharger I bet.

 

i thought the diameter changed on the lugs?

 

The vent is standard on the MCS - battery ventilation or "let more exhaust noise into the cabin", your choice !
Maybe the low fuel warning is at the same level, but lower mpg for the MCS?

 

Yeah, from M12x1.5 to M14x1.25.