Well a guitar can never ever be in tune at every point on the neck why not use the best alternative - now some companies are making guitars having frets that are literally crooked to make every point on the neck in tune .. Try equal temperament tuning if you have never heard of it.. Its a trade off much as Jerrys tuning is they all are do to the physics of stringed instruments the piano is the same way... It is never really in tune... This was set in stone back in the 1600's that all stringed instruments would always be out of tune its just again physics
For those of you that do not have the equal temperament instructions here they are I am not saying this is the answer as their is not one accept as I said to actually make every fret crooked across the neck...
Equal Temperament tuning...
Tune the Open E and e strings so that they are in perfect unison. The open high e string should be in unison with the harmonic at the 12th fret of the low E.
Tune the E note on the 2nd fret of the D (4th) string to the harmonic at the 12th of the E (6th) string.
Tune the D note played on the 3rd fret of the B (2nd string) against the harmonic on the 12th fret of the D (4) string.
Tune the D note played at the 7th fret of the G (3rd) string against the harmonic on the 12th fret of the D (4) string.
Check the harmonic at the 12th fret of the G (3rd) string against the G note played at the 3rd fret of the high e String. If this is not in tune, something has gone awry in a previous step.
Tune the harmonic at the 12th fret of the A (5th) string against the A note played on the 2nd fret of the G (3rd) string.