What is it that makes one unit a 12 SEER and another a 16 SEER? What is it that makes the difference?
The amount of energy it takes to produce the same amount of cooling. The higher SEER rating a system has, the less it costs to operate.
Government is a disease...
...masquerading as its own cure
Ecclesiastes 10:2 NIV
Indoor coil size
Outdoor coil size
Non-bleed TXV vs bleed type or piston
Yep, all of that, Its really just a matter of Watts and how many it takes to produce the Btuh's. The lower the better. The items the Bald one pointed out are means to lower the watts required. For instance on an outdoor coil, a much larger coil will use less fan to reject the same amount of heat. The smaller fan motor uses less watts.
Matched Equipment: condenser, evaporator and the refrigerant control (demand a TXV) "are both SEER and EER rated." The SEER rating is meaningless if the matched system can not meet its EER rating due to ductwork problems or half a dozen other screwups!
Its operating EER is the easiest to test check and document. The operating performance of every installtion should be checked and recorded.
For example: due to ductwork or something else, you might have matched 13.5 rated EER/14-SEER equipment that is only performing at 9 EER. In that case it will be lucky to operate at 10 SEER.