I've gone into NRT when the extra airfare cost reached the cost of a Japan Rail Pass, so if I can save +/- $270.00. If I have other long distance travel, that calculation might vary. I rather enjoy riding the shinkansen so the extra time doesn't bother me as long as I arrive in Japan in time to get to Kyoto before the trains stop for the night. YMMV.

The best alternative used to be NGO but the airlines I use stopped flying there from the west coast several years ago.

I refuse to try to shoehorn my 6'5" frame into a Japanese domestic economy seat.