Final three days of a month in Japan advice

Hello, I'd really appreciate your thoughts and advice.
I'm trying to finish an itinerary for my wife and I (mid sixties) with our final three nights of approx one month in Japan (which coincides with Rugby World Cup).
We have about week in Hokkaido (for Wallabies vs Fiji) staying in Sapporo, Biei, Lake Toya and Hakodate (using a hire car to get around).
We then activate our 21 day Japan Rail pass to travel south and spend just two nights in Tokyo (Wallabies vs Wales). Train to Matsumoto for two nights then Kanazawa for two nights, Kyoto for 4 nights, Kurashiki for two nights, Miyajima for two nights then Onimichi for another two nights (while I cycle the Inland Sea route). This much is locked in with no real variation possible.
We then have three nights before departing from Narita. As you may have gathered, we don't love cities but can appreciate what they have to offer. Hakone was on our list but expensive and very mixed opinions from what I can gather. I was thinking maybe Osaka or perhaps a bit more time in Tokyo. Is there another place you could recommend? Having never been to Japan it is so hard to get to a final, happy decision. Perhaps further south before the train trip north? Is it a shame to miss Osaka completely? I'd appreciate any thoughts - thank you.
P.S. We fly out at 7.30 p.m. on the 17th October, so plenty of time to travel on that day.

Endless possibilities. But Osaka wouldnft be on my top list. If city, I think Tokyo is way more interesting than Osaka.

Here some ideas:
- Takamatsu in Shikoku with day trips to Teshima and Naoshima. I would need 3 days for that. And then fly to Narita
- Nara and Daytrips around Nara. Easily also 3 days for me. Big Nara Prefecture fan: http://bicycletraveljapan.blogspot.com/search/label/Nara?m=1
If you are less of a Nara fan you could combine it with Koyasan
- Beppu and Yufuin if you like onsen. But I would do that after Miyajima and before Onomichi. Just a little bit more logical
- Lake Biwa: Miho Museum, Otsu, Hikone Maybe 2 days could be enough
http://bicycletraveljapan.blogspot.com/search/label/Shiga?m=1
- Izu peninsula and stay somewhere like Shimoda or are und Shuzenji. Great place for onsen. It is reachable by train, but for exploring the peninsula itself a car would be better. If you like hiking thatfs a great place
- Kamakura if you like Kyoto you could also like the old city of Kamakura. Most people just go there for a day or half day trip. I could stay a week.

I guess I could go on. From the list above I would say that the stint in Takamatsu or the one in Izu are the ones that offer new experiences you hadnft had yet in some other form during your trip: modern art on Naoshima &Teshima or onsen and hiking on Izu.

Enjoy your trip to Japan!

I'd second the suggestions for either Nara (you could also go to Uji on the way there or back); or Lake Biwa. You might even like two nights in Nara, and one night at Hikone on Lake Biwa and see Hikone Castle.

My other suggestion would be head north of Tokyo and have a night or two at Nikko.

Go the Wallabies!

And have a wonderful time in Japan.

Above suggestions are pretty good. I donft think you need to be concerned about back tracking from Miyajima to Onomichi, then to Kyushu. Since you have the time and JR Pass - just hop on the Shinkansen and back track all you want.

One option is to leave the last 3 nights open and decide as the time approaches. You could go back to places you want to explore more (like Kyoto, which I would want to stay more than 4 nights).

Nara is not to be missed, but 3 nights may be too much. Most people visit Nara as a day trip from Kyoto.

Other suggestions: Hagi and Tsuwano; Wakayama (Nachi Falls); Ise; Hakone (I enjoyed it very much); etc.

Thank you very much for taking the time to help with your experience and advice. I posed an impossible question to answer but you have provided many suggestions which I simply hadn't considered or known about - and also confirmed that perhaps Hakone isn't so bad after all. Like Bike, I'm passing your blog onto my touring cycling friends, they will love it. Who, yes indeed: Go the Wallabies and we certainly believe we will love our time in Japan. 092, thanks also for your thoughts on Hakone and other advice about using the JR Pass. All greatly appreciated.