Plan 23 day itinerary-Kyushu/back to Tokyo

We plan (2 of us, 46 yo, no kids) to fly from Brussels via Tokyo directly to Fukuoka. From there, we want to visit Kyushu. After exploring Kyushu, we want to make our way back to Tokyo and stay for about 4 of 5 days for the last part of our holiday.

We have been to Japan before, starting in Tokyo, going to Kyoto, Nagoya, Hiroshima, Miyajima, Takayama, Kanazawa, Toyama, Matsumoto and back to Tokyo. We love Tokyo, so that is why we really want to end there with a couple of days.

However, the rest of the trip is a bit of unknown to us. We have been reading a lot, so we have a lot of info available, however it is really difficult to refine an itinerary.

We have some questions:

How many days would you advise to spend traveling Kyushu (taking into account we have 21 full days in Japan of which we want to reserve 4 or 5 days for Tokyo)?

How could we make our way back to Tokyo via an interesting route, avoiding sites we have already been to (Kobe, Osaka, ...)?

You could spend the whole 3 weeks in Kyushu and not see it all. You really need to decide what you like and where you wanna visit. This website has heaps of info to browse through.

Just allocating a day to each of the bigger touristy cities in Kyushu eg- Fukuoka, Yufuin, Beppu, Kagoshima, Nagasaki, Kumamoto is 6 days worth.

Start adding in some side trips like Miyazaki, Nichinan Coastline, Unzen, Asosan, Ibuzuki, Kita-Kyushu/Moji port, Takachiho and you'll jump up to 13 days easily.

then for coming back via a different route from what you have already done. Again it is up to what you like. Lots of info on this website. The north beaches side of Chuguko eg matsue, tottori, kinosaki-onsen etc would work.

If you take flight into consideration, you can go as far as Hokkaido or Okinawa. Now Japan's two legacy carrier ANA and JAL provide discount tickets for foreign tourists which is 10,800 yen one way. For example you can fly from Fukuoka to Sapporo and then Sapporo to Tokyo's Narita or Haneda. Some LCCs provide even cheaper fares.

Japan can be divided (as for the scenery and culture) into two: Okinawa and other part of Japan. Other part of Japan can be divided into two: Hokkaido and other part of Japan (which includes all places you have already visited and Kyushu). So if you want to see many aspects of Japan, you might better see these two places. If you are coming from Belgium, Okinawa might be more interesting, since it is tropical islands. Of course it depends on your preference and the season you will visit. When will you travel?

Thanks for your insights. We plan to leave Brussels September 5th and return September 27th.

Indeed, 3 weeks in Kyushu might not be enough.
How will you travel around?
Wasting time with catching train, bus and hotel schedules OR use your own transport (rental) and see the things you otherwise won't see? You have been to Japan before you mentioned. Time to move away from the typical tourist spots.

We were not planning on self-driving Kyushu, but having read multiple posts where people are positive about driving in Japan, I think we would want to drive around Kyushu for about 12 or 13 days. Starting and ending in Fukuoka. Maybe thinking about picking up the car in Nagasaki after traveling there by public transport. We do not need to drive around in Nagasaki, but when leaving to continue our trip around Kyushu, picking up the car. After the trip around Kyushu, we would drop off the car in Nagasaki again, taking the train to Fukuoka or even directly from Nagasaki direction Tokyo.

The northern sights are fairly easy to access using public transport. Also Kumamoto and Kagoshima. But most of the south and centrally located sights are much easier to access using a car. It really depends on what you wanna see.

You could quite easily do Fukuoka, Nagasaki and Beppu/Yufuin by public transport. Then hire a car in Oita, and do Takachiho, Asosan, Miyazaki, Nichinan Coastline and Kagoshima. returning car back to Oita.

I agree with @hakata14 I would use the trains to visit the northern parts of Kyushu and maybe hire a car in Kagoshima. I was there last spring & the places I enjoyed visiting the most were, in no particular order:

Nagasaki: all of it but particularly the Glover garden, Dejima & Mount Inasa night view. I also went to Yoshinogari Historical Park which is between Nagasaki & Fukuoka.
Fukuoka: Dazaifu & museum, Uminonakamichi seaside park.
Kagoshima: I used it as a base but need to return it's a great place
From Kagoshima I side tripped to the Chiran Peace museum for Kamikaze pilots & on to Nishi-Oyama station which was a great day out.

I only scratched the surface & will definitely be returning.

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.

Many options.

Enjoy your trip to Japan!

We have tried to create an itinerary, trying to cover most of Kyushu in about 12 or 13 days, using a car as from leaving Nagasaki and returning the car in Fukuoka. I saw from the Tocoo website that the one way drop off fee is not that expensive (about 7000 JPY). That for us is worth it over driving in and through the larger cities.
This is what we have now:
Sept 5: Brussels - Fukuoka (arrive early afternoon)
Sept 6: Fukuoka - Fukuoka
Sept 7: Fukuoka- Nagasaki 
Sept 8: Nagasaki- Nagasaki 
Sept 9: Nagasaki - Kumamoto (pick up rental car / car ferry to Kumamoto)
Sept 10: Kumamoto - Kagoshima
Sept 11: Kagoshima - Kagoshima (daytrip car ferry to Sakurajima)
Sept 12: Kagoshima - Takachiho (via Miyazaki coastal road)
Sept 13: Takachiho - Kurokawa Onsen (mount Aso)
Sept 14: Kurokawa Onsen - Kurokawa Onsen (Kuju NP)
Sept 15: Kurokawa Onsen - Yufuin
Sept 16: Yufuin - Kitakyushu (via Beppu / Takegawara Onsen sand bath)
Sept 17: Kitakyushu - Fukuoka (return rental car)
Sept 18: Leave Fukuoka towards Tokyo

Does this itinerary make sense? We are trying to make the most out of the rental car to cover most of Kyushu.

For an "interesting route back to Tokyo", you might consider spending some time on Shikoku.

The other option we were thinking about to make our way back is via Japanese Sea side (Fukuoka, Hagi, Izumo, Tottori, Osaka, Tokyo)

Also, while it is not on the way, Sapporo is only a short and cheap plane ride from Fukuoko and Tokyo, and Hokkaido weather will be very pleasant in September. That might be kind of fun to hit both ends of Japan in one trip.

You can fly from Fukuoka to Sapporo for $50 + luggage fees on airlines like peach, skymark and jetstar. It's about the same to fly back from Sapporo to Tokyo.

Sapporo does sound appealing, but what would you suggest? We have about 3,5 days, would you just visit Sapporo, or travel around? Is 3,5 days enough then?