Sean, you are absolutely right on target. We hear differences and we don't know to what they should be attributed but we are confident that they exist. I think that's a given for most of us. It is where we go from there that makes the difference in our long-range understanding of good sound.
In the short run, these matters are easy: Try it. Like it? Got the cash? Do it.
In the long run, we need to continue to explore and measure and poke and prod and make careful comparisons. We need to be unafraid to put our subjective comparisons to the test, knowing that testing methods are imperfect but likewise not without value. We need to candidly acknowledge that:
(1) Some clearly discernible differences in sound exist that cannot be measured or quantified...at least not yet, possibly never.
(2) Some perceived differences probably arise from a whole lot of extraneous factors such as how much we paid for our gear or how many hours we spent tweaking it.
Exploring these possibilities ought not be so intimidating to either EEs or GEs that they go into conniption fits of character assassination every time they come face to face.
Augustine said it: Love God and do as you will.