Itinerary Check + Questions for first trip to Japan (21 Days)

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My girlfriend and I will be traveling to Japan in October as an uni graduation present from our parents! We are soo thrilled for this opportunity, but it will be the first time we are traveling to Japan (or out of the country on our own) so we could use some advice. 

Firstly, here is our itinerary so far: 
- Oct 3: Arrive in Tokyo, Check into AirBnB (Near Ikebukuro Station), Otome Road, J-World Tokyo
- Oct 4: FMA Exhibit (@ Tokyo Dome), Akihabara (Tokyo Anime Center, Imperial Palace 
- Oct 5:  Tsukji Market, Ginza District (Pokemon Store) 
- Oct 6: Shinjuku District, Dinner @ Den 
- Oct 7: Shibuya District, Night out in Shibuya District 
- Oct 8: Day trip to Kamakura 
- Oct 9: Asagaya Anime Street, Ghibli Museum 
- Oct 10: Free day for exploration? Roppongi? Nakano Broadway? (Suggestions?) 
- Oct 11: Traveling to Nagano and staying in the area for the night (finding a Ryokan to stay in) - -
- Oct 12: Traveling to Kanazawa (staying in a Ryokan)
- Oct 13: Stopping in Fukui and then continuing to Osaka, Umeda Sky Building, Grand Front Osaka Mall 
- Oct 14: Osaka Castle, Downtown Area, Dinner @ Kashiwaya, Night Out 
- Oct 15: Free Day to explore any places we feel like? Yamazaki Distillery? (Suggestions?) 
- Oct 16: Travel to Kyoto (Low key day getting acclimated), Explore the nearby areas
- Oct 17: Historical Day 1: Fushimi Inari Shrine, Kiyomizu Temple, Gion, Yasaka Shrine, Others?/Suggestions?), Nishiki Market
- Oct 18: Historical Day 2: Nijo Castle, Kyoto Manga Museum, Kyoto Imperial Palace (Others/Suggestions?) 
- Oct 19:
- Oct 20: Uji, Nara (Busy Day)
- Oct 21: Ine, Kinosakionse Onsens 
- Oct 22:
- Oct 23: 

As you can see, there are still some holes in our itinerary and we wanted to leave one free day in each city to leave room for any suggestions from locals we may receive. 

Regardless, I have some questions: 

(1) One question I definitely need help answering is: Is the 21d JR Pass worth it for this itinerary? It is NOT cheap so I want to make sure it's really worth it before we invest that much.. I tried using the Calculator, but it was very confusing :/

(2) Is there anything on that list I should reconsider? Either because it's not that great or too far.. 

(3) Other recommendations? We definitely have Otaku interests (which can be seen in our Tokyo itinerary haha), but we also want to get the REAL Japan experience while we're there.. Things we're unsure about are:
  • Raumen Museum
  • Yamazaki Distillery
  • Nakano Broadway (kind of out of the way but probably worth it for 2 weebs, right?)
  • Nanki-Katsuura (Saw recommendation in this subreddit from a Japanese local about amazing tuna and onsens - 2 things we love - but it is SUPER far from Kyoto)
  • Roppongi?
(4) Last question: Good Hiking places around Kyoto? Would love to dedicate one of those free days in Kyoto to hiking in Japan's beautiful nature 

Thank you in advance!
Mari Takahashi Mari Takahashi, Living in Japan

Answered over 3 years ago

(1) About the JR Pass
It will be so much valuable if you are going to use JR Shinkansen and express trains. It seems like you will be traveling a lot within Japan, so I think it will surely cover all your transportation cost. For your information, one-way Shinkansen ticket from Tokyo to Kyoto costs more than 10,000yen if you purchase normally. (I am a local Japanese, and I always want to buy Japan Rail pass!!)

(2) About the itinerary
I'm not sure if you can spend a whole day in Shinjuku and Shibuya. Shinjuku and Shibuya are kind of alike: they are both shopping, dining, nightlife districts. If you are not looking for some particular things, I don't think you need to dedicate a whole day to each. Instead, if you are in Tokyo, exploring Yanaka (or Yanesen) district may give you a different aspect of Tokyo. It's an old town near Ueno, having a nostalgic atmosphere with great restaurants and bars. Or, take a day trip to Kawagoe or Sawara to feel the old Tokyo (around Edo-period) atmosphere. 
Kamakura is a beautiful coastal town, so you should really visit there. (Kamakura is so big, and I always feel I should have stayed a night when I go there. Staying near Kamakura might be a good idea, too)

(3) Other recommendations
I partly stated in my answer to (2) :)
Nakano Broadway will be fun if you are an Otaku! lol  There are lots of small shops selling some old, rare, collectible goods. They may not have new ones so much, when I went there (it was more than 5 years ago), they mainly had good from old anime such as the 60s, 70s, 80s, etc. 
Not sure if Roppongi is fun, it's just a district with bars and clubs. I haven't explored much in the district at night, so I should leave the advice from some experts. 
It seems like you still have some free days. How about Hiroshima and Shikoku? Hiroshima is an important sight in the world history, has famous Miyajima Shrine, and also has great food; oyster, Hiroshima style Okonomiyaki, etc. Kurashiki in Okayama Prefecture is close to Hiroshima, too. Shikoku is an island containing 4 prefectures; Ehime, Tokushima, Kagawa, and Kochi. Beautiful views, great food. Many historical temples and it's a destination for Buddhism pilgrimage. (Shikoku Tourism website:

(4) Hiking places around Kyoto
Not exactly around Kyoto (you'll need to travel from Kyoto actually), but one of my friends went to Kumano Kodo from Kyoto. Kumano Kodo is a World Heritage forests with a beautiful shrine.
If you are going to Kamakura, Kamakura has some hiking trails, too.