Equal temperament was invented for piano and keyboard instruments. It's function was
not to create the best sound for harmonies (in fact it made harmonies sound
less sweet)- but rather it was invented so that the instrument could play in various keys and still sound as good as possible. It created a series of compromises, which makes all the intervals more or less equal between notes. In a more natural setting, the notes of a scale will have longer intervals between some notes and shorter intervals between other notes. When staying in ONE scale, this is very pleasing sounding, and the harmonies there are the most pleasing. But change to another key without moving those intervals and everything will sound slightly 'off'. On fretless instruments (violin) or instruments with movable frets (lute) the player compensates automatically for this with subtle finger placement differences, but with fixed frets (or with piano where you wouldn't want to retune every time you change keys) you cannot compensate much.
So equal temperament was invented for keyboard/piano, and fretted instruments that play in multiple keys (guitar, banjo, mandolin...) all followed suit. All these equal tempered instruments could play nicely in sync with each other. This was an organized shift in an effort 'standardize' all instruments and enable them to change keys quickly with fewer problems. But overall the equal intervals produced a total sound that was slightly less sweet and perfect, yet solved a lot of problems for the muscians playing together in various keys. Throw a just-tempered instrument (with fixed frets you cannot move) into the group to play with them, and it would sound slightly 'off'. And with fixed frets you cannot fix the problem by retuning, because the frets are dictating the invervals between notes. You can't
tune back and forth just temperament or equal temperament...and they are not
tunings. If you are
fretless you can switch back and forth using your finger placements (but you have to be able to hear the very slight differences in intervals)...but if you have
fixed frets you cannot change the intervals by re-tuning open strings- the frets will be permanently placed for a particular temperament, such as just or equal.
Over the 150 years or so years since equal temperament has become the standard, people have grown up being used to hearing equal temp. in all popular music. So nowadays, most people who hear music being played in just temperament (or any other non equal temp. for that matter) find it odd sounding and often think the notes are 'out of tune'. In fact, the notes are slightly more IN tune than in equal t., but sound odd because they are not what folks are used to hearing anymore. If you listen to a group of musicians specializing in archaic music and playing on historically accurate reproduction instruments, you might think they are playing 'out of tune' but you attribute that to their 'old' instruments that 'can't play in tune'. Lots of people say the same thing about old recordings of fiddlers too- that they are 'playing out of tune'..when in fact in most cases they are playing in older scales using older intervals. Of course, that's not to say that a few of them aren't actually playing out of tune!

But most of the time it's due to the subtle interval/temperament differences.
Here looks like an interesting book, titled
How Equal Temperament Ruined Harmony: And Why You Should Care:
http://www.amazon.com/Equal-Temperament ... 715&sr=8-1
