Flexibility & schedule matter since we have the ability to leave whenever we want. Time is of the essence so that I complete a journey in 6 hours instead of 10. Car makes it easier to haul the wife's wardrobe. So yes, its a combination of everything.

Driving is something I have done all over the world & am pretty comfortable with it. We have rented camper vans & driven across Europe & North America for weeks. Its what we have always used as our main mode of transport everywhere we go. I'm sure the Tomei expressway can be horrendous in holiday traffic but if you ever drive in India then you would be used to it. Takes me over an hour to get back home every evening when the distance is less than 5km.

Having said that & after getting all the information in this thread, we are now leaning towards taking the Shinkansen from Tokyo to Kyoto & on our way back we fly Osaka to Tokyo. Flying on the way back gives us an extra night either in Kyoto or Osaka as we can take the first flight in the morning to catch our connection back to Delhi a few hours later. Taking the train or driving will require us to be back in Tokyo the night prior to our flight back home.