There is a contributor to the Frets.Net Forum who talks at length about nut compensation. It is not a universally accepted idea but he is completely sold on it.

I can't see the point myself. The guitar, like the keyboards, is an instrument that has compromised tuning at it's heart. It is always going to be a bit out of tune. If you can't be doing with that you should play an instrument like the fiddle or the fretless banjo where, skill allowing, you can always play in tune.

It's a trade off between being perfectly in tune for one key only or slightly, but consistently, out of tune all the time.

I can live with the guitar as it is.