Anyone with knowledge on JR routes?

Hello clever people!

I'm headed away to Japan for almost 3 weeks and would love your advice on which JR Area passes or tourist passes I should get (if any?). I'm quite overwhelmed by all the calculations so any help would be so greatly appreciated. My itinerary is below, all feedback is welcome!

Day 1. Australia to Osaka
Day 2. Osaka to Tokyo - Shinjuku and Shimokitazawa
Day 3. Tokyo - Shibuya / Harajuku / Akihabara
Day 4: Tokyo - Kappabashi street, Nakamise-dori and Sumo Tournament
Day 5: Tokyo - Day trip to Kamakura
Day 6: Tokyo - Day Trip to Tokyo DisneySea
Day 7: Tokyo - Day Trip to Lake Kawaguchi
Day 8: Tokyo - Day trip to Nikko
Day 9: Tokyo to Nagoya - Pokemon Cake, TeamLab Borderless, Train from Tokyo to Nagoya
Day 10: Nagoya - Day trip to Tsumago to walk Nakasendo Trail to Magome, return to Nagoya and train to Kyoto
Day 11: Kyoto - Temples
Day 12: Kyoto - Day trip to Arashiyama
Day 13: Kyoto to Ine and Amanohashidate (staying in Amanohashidate)
Day 14: Amonhashidate to Kinosaki Onsen (staying in Kinosaki)
Day 15: Kinosaki to Kyoto - Gion and fushimi inari
Day 16: Kyoto - Day trip to Kibune and Kitano Tenmangu Shrine market
Day 17: Kyoto to Himeji and Hiroshima (staying in Itsukushima, Miyajima Island)
Day 18: Miyajima Island to Osaka
Day 19: Osaka - Universal Studios
Day 20: Osaka - return to Australia

Did you consider flying Kansai to Tokyo?
In reality, you are only staying in two areas (Tokyo and Kyoto) for your trip apart from a diversion to Hiroshima, so the Kansai/Hiroshima pass might work for that piece.

Days 17, 18 & maybe more: JR Kansai Hiroshima pass, which already pays off with a round trip from Osaka to Hiroshima. https://www.westjr.co.jp/global/en/ticket/pass/kansai_hiroshima/

Note that this does not include the use of shinkansen between Kyoto and Shin-Osaka.

This pass also covers Amanohashidate and Kinosaki onsen, so if possible, you should rearrange your planning to fit them in the 5-days window.

You should mention

Tokyo to Shin-Osaka (via Shinkansen) is allowed only by (nation wide) Japan Rail Pass and Japan Rail Pass is too expensive for most of the travelers.

You must consider validity period, such as 4, 5 or 7 days, for your candidate regional passes.

Regional passes will be useful if you make rather long trip using Shinkansen. Commuter trains within cities are negligible since they are very cheap and sometimes not run by JR companies.

In your itinerary, you don�ft need to think about rail passes on Day 1 to Day 12, Day 19 and Day 20.

Day 13: Kyoto to Ine and Amanohashidate (staying in Amanohashidate)
Day 14: Amonohashidate to Kinosaki Onsen (staying in Kinosaki)
Day 15: Kinosaki to Kyoto - Gion and fushimi inari
Day 16: Kyoto - Day trip to Kibune and Kitano Tenmangu Shrine market
Day 17: Kyoto to Himeji and Hiroshima (staying in Itsukushima, Miyajima Island)
Day 18: Miyajima Island to Osaka

Kansai-Hiroshima Area Pass 17000 yen

https://www.westjr.co.jp/global/en/ticket/pass/kansai_hiroshima/

covers all areas, but this is valid for only 5 days so you must pay separately Day 13 or Day 18 (Day 13 is cheaper).

Another pass is Sanyo - San'in Area Pass 23000 yen

https://www.westjr.co.jp/global/en/ticket/pass/sanyo_sanin/

which covers 7 days. I would recommend this pass, since this pass allow you more freedom (JR train travel on Day 12 or Day 19, travel by Shinkansen as far as Hakata, etc.).

Other comments.

I would skip Gion and Fushimi Inari because of the overtourism.

I think the most important part of Kyoto is Higashiyama district from Ginkakuji to Kiyomizudera. I recommend to visit this area for 2 days. Day1. Early morning to Kiyomizudera and walk to Subway Keage station. Day 2. Early morning to Ginkakuji then walk to Nanzenji to Subway Keage station.

Day 15 - Fushimi Inari might not be the "best" shrine in Kyoto, but it is still a good spot to visit.
Gion - other threads and forums wonder what's the point and given how badly people behave and that there is really limited things to see that differ from the rest of the city - over-rated, easily skipped.