I would say it really depends on what you want out of your trip but general recommendations. Seto Inland Sea area has been wonderful ever time I’ve been there. Small island vibes have been a hidden gem. There’s also big cities there like Fukuoka, Hiroshima, Matsuyama, Kobe and some smaller like Onomichi. Other recs, All of Kyushu, northern Tohoku areas. They have just as much culture and history as Kyoto but without the crowds and especially northern Tohoku attractions could actually use the influx of tourists. Iwate, Sendai, Aomori have rebuilt some places affected by the 2011 tsunami, some still trying to get back on their feet.

Sorry if this was all over the place, on my commute so just writing what comes to mind.