[neonscribe]

No, the Maj3 interval between the 2nd and 3rd strings on the guitar is unrelated to this issue. It's just the fret spacing on the guitar that causes it to have equal temperament and therefore makes chords slightly "out of tune".

[elihu]

Incidentally, a just (non-tempered) guitar fingerboard might look something like this:

http://jsnow.bootlegether.net/cbg/fingerboard_at_a.svg

I swapped fingerboards on an old Harmony Archtone with one based on the above design. Admittedly, 20 notes per octave may have been a bit much; it's kind of awkward to play. The next one I do will be simpler. Sounds nice, though.

[gnaritas]

Just remove the frets, problem solved.

[elihu]

Fretless is difficult to play accurately, especially for chords. Also, you get a louder sound from frets because your fingers aren't muting the strings quite so much.

[gnaritas]

Of course, but it does solve all such intonation problems.