Osaka > Kyoto > Tokyo

If you are traveling in Japan one way only, then a JR Pass would not pay off for your itinerary. So, you could pay regular fare, totaling just over 14,000 yen. An alternative is flying on a low cost carrier like Peach or Jet Star, for about ¥4,240 (about US$35). Another way is by bus, but that is extremely slow. Time saved by flying would mostly be eaten up by going to/from the airports, but the money savings is still real.