Trained ears.

In your case it should be pretty simple - use well recorded piano music that you know well and ask yourself which system or change gets closer to the sound of a real piano in a real room

in my case And given the types of music I am most experienced with I use a variety of rather sparsely recorded folk music and look for system changes that get closer to the experience of real musicians in real space. 

Listening for gross frequency response issues or the top and bottom of the range is besides the point if the system is messing up the small details

This is a nice tool to play with.

http://harmanhowtolisten.blogspot.com/

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.

Agree with the above posts, plus sitting in the sweet spot with eyes closed helps quite a lot. Also, if you wear glasses, remove them.

Tom