Okinawa to ?

Hi there, I’m doing a 3 week stay in Japan (May 29-June 17) and I’m starting in Okinawa. I am confused where to go after that. I see that Takachiho Gorge is overrated (darn). I debated Nagasaki but it’s far and not sure about logistics. I want to spend a good chunk of time in Tokyo and have some time for Kyoto and Osaka but 3 weeks gives me plenty of time to do that. Any suggestions of more local cities I could explore?

I am seeing a rugby game in Tokyo June 6 and I do have my IDP but I’d prefer not to drive. I love train and ferry rides. I do like off the beaten path and smaller towns, I’m open to anything. Also any Okinawa/Tokyo/Kyoto accommodations are greatly appreciated (max $100/night)! At this point only plane tickets are bought haha, thank you!