A suggestion made elsewhere is to intonate the guitar to be "correct" at the 7th or even 5th fret. It's all a compromise, but you might find that one to be easier on your ears. Arguably, the only reason we became wedded to 12th fret intonation was that in the era before electronic tuners, we could use the 12th fret harmonic to compare to the fretted note at the same place.