Hello.
Iam from Sapporo(north big island of Japan)not from Tokyo or Kyoto..
But I can say if you want to do that route , you would be better to buy a JR Ticket at firrt arounf Tokyo, Kyoto.Hiroshima etc.It is on the TOKAIDO Bullet Train rain.
Talking about Tokyo Area,,Ummm, it is hard to point out where.which.
So need mor idea what you want to do and have the experience etc.
Of course, just sightseeing all around of Tokyo is Ok for your days, I think.