Since there's only one line on the Kyushu Shinkansen, you would be seeing the same things twice.

You may want to look into returning via one of the conventional train lines and taking in Nagasaki and Mount Aso (west coast) or Miyazaki and Beppu (east coast--what Yellowstone Park might have looked like if private interests had each been allowed to buy a geyser).

If you are returning to Tokyo, I suggest taking the "back way" from Nagoya on the Chuo Line. This goes through some different scenery behind Mount Fuji and is less developed than the Shinkansen route. You end up at Shinjuku Station.

Even the non-Shinkansen trains in Japan put Amtrak to shame.