Planning. A good HVAC technician will not install a system based on rules of thumb, intuition, or past experience. Years of experience might give them a good idea of what's needed, but a good tech will still run the numbers.
Not properly sizing the equipment, is the biggest mistake folks make. When it comes to efficiency, this is probably the largest detriment. Calculating the heating/cooling load is not easy, and cannot be done simply based on square footage. Unfortunately, it seems as though loads of HVAC companies only ever consider square footage. X square feet = Y Btu/h. This is completely wrong, and will not lead to the most efficient system being installed.
If a system is being replaced, a bad tech will simply use the existing "plumbing" (duct work, vents, etc.). Whereas a good tech, will determine if the old plumbing can be used, but won't use the existing plumbing simply to save time/money (unless told to by the employer (you)).
A good tech will also be up to date on the latest technologies, codes, and industry standards. It's easy to get stuck in a rut, and always do the same thing the same way (even good techs fall into this sometimes). To be a good tech, you have to be constantly learning and evolving. At the same time, you can't always follow the latest fads. The latest and greatest isn't always the best approach. A good tech will research new technologies, to gain a better understanding of how it can help them do their job.