Convenience & simplicity aside, how expensive is it? Not necessarily compared to driving, but just in general. When I went to Japan a long time ago, I remember being kinda shocked at the cost compared to the JR Pass for tourists (which included the Shinkansen), but part of that was to give tourists a huge incentive to spend some money outside of Tokyo, I'm sure, but I remember some fares feeling expensive for people just to head into the city for a night out...
I don't think it's expensive, but then again I'm comparing it to train prices in Northern Europe, which is just painful. There, I'm used to pay for the ticket through gritted teeth. In Japan I can pay for a ticket + limited express (better train w/booked better seat) for a 45 minute ride for what I would pay for a pint of beer at home. Totally worth it. The Shinkansen for a 90 minute ride is not cheap, say ten beers.. Northern Europe beer prices, mind.