Trained ears.

Complicated. First of all I try to figure up what annoys me most in what I hear and then go from there. Drive flow and coherence are what should be done right before everything else, I believe. Assuming that speakers are more or less okay, this means that you start at the source. And the best source is tape.

What is complex is to tune the system like an instrument. You have a few components working together that must become the one. This does require experience and some knowledge in addition to hearing. And don't forget the room - it is probably the most important single component, provided the rest are good enough. One wrong set of cones under one component and the system is out of tune to various degree, wrong platform under turntable and it's no good, wrong or not quite right power cord on your Studer deck and something is lacking.