I agree with the previous posters that you could spent 3 weeks in Kyushu alone, so let me try to answer your other question about an interesting route back to Tokyo.
I think there are 4 major options:
1) just fly back
2) go back by Shinkansen on the "normal" route along the coast of Hiroshima through Osaka, but stopping at places you haven't visited in previous trips. E.g. Okayama, Bichu-Takamatsu, Kibi plain, Kurashiki, Teshima, Naoshima, Inujima, Inner Nara prefecture, Koyasan, Hikone, Ise, Izu peninsula... Depending on how many places you stop by this could also take something around 10 - 14 days.
3) go back through Shikoku, i.e. do a week in Shikoku. You can either fly to Shikoku, or there are also ferries available between some ports specially on the Western side of Kyushu. E.g. you could go to the South East part of Shikoku, go to Shimanto Gawa and then travel through Shikoku. Read up the part on Shikoku notes on this web page, but you could easily spend another 10 days in Shikoku. I specially liked the garden in Takamatsu and Naoshima and Teshima. Also if you are into cycling you could ride the Shimanami Kaido. https://bicycletraveljapan.blogspot.com/2017/11/part-10-day-48-49-ridi...
4) Travel back to Tokyo on the Japan SEA side of Honshu, going through much less travelled places such as Hagi, Matsue, Tottori, Fukui, Kanazawa and then back to Tokyo, or even on to Sado island. If you do that I would say you should spend there at least 10 days. Public transport is available on the Japan sea side, but MUCH slower.
Enjoy your trip to Japan!