I suggest you read, for further information on how temperaments work, and how psychoacoustic phenomena work in general, the seminal work on the project, On the Sensation of Tone, by Hermann Ludwig Ferdinand von Helmholtz, 1863, which I have read in first edition when I was in college in the early '80's.
No, I agree, no physical system is perfect. I could go on and completely use up all the available bandwidth explaining how all the different systems work, from Buzz Feiten, to Gibson, to Earvana, to Delft, to the Renaissance "mean tone" frets, to the various folks who place staggered pieces of frets up and down the fretboard to achieve their variety of temperament. And then there's all the keyboard temperaments: equal, meantone, quarter-comma, the various Werkmeister and Young temperaments, ad infinitum, ad nauseaum.
Now, how about adding to that all of the inherent intonation quirks that various rock-n-roll band, concert band, jazz band and orchestral instruments have that must be accommodated, from flat 5th partials on most brass; sharp 6th partials on euphoniums, throat tones on clarinets that are never in tune, sharp A's on saxophones, etc., when those who play those instruments don't necessarily adjust themselves in the mix.
And finally, how to split the difference on instruments, like old pianos, that are just plain out of tune.
No, of course nothing is perfect. But there is a lot more to it than the summary comments that have been made so far. And I have done for my playing what works so I can do my job properly with whatever ensemble I'm in. Do I tweak tunings? Yes. Do I listen for voices and orchestral strings that tune "pure" instead of tempered? Yes. And so it goes. Even if the bass is not the problem. The bass usually gets blamed for it because of a combination of either the conductor or the egos of the other players pointing fingers. So the bass has it doubly hard.
So I have my shims set so I have a only a minimum of amount of adjustment I have to do to accommodate all the above, still provide a good foundation, and more.
Now, where was that Cowboy open C chord?
