From my perspective, as an easily distracted/lost person, the biggest advantage of the JR pass was that when I forgot to get off the train at the correct stop I was not suddenly stuck explaining to a conductor in a language I don't speak why I was riding a train I wasn't ticketed for, and I could just get off at the next stop and take the first train going the other way. You may be a more competent (or less jet lagged) traveler than I am, but the flexibility is a nice bonus even if the if-everything-goes-according-to-plan savings are small.