Second trip to Japan - suggestions

Hello there!

I've been to Japan for the first time 2 years ago and my itinerary was mostly inspired by the Japan Guide. During it I was able to see/visit:
- Tokyo (Asakusa, Sensoji, River Cruise, Hamarikyu, Odaiba, Imperial Gardens, Akihabara, Shibuya - crossing, Hachiko, Shinjuku - strolling & Metropolitan bld)
- Nikko (Chuzenji, waterfalls, Shinkyo, Rinnoji, Toshogu)
- Kamakura (Engakuji, Kenchoji, Tsurugaoka Hachiman-gū, Kōtoku-in, Hasedera, Enoden)
- Takayama (Hida Folk Village, Takayama Jinya, Takayama Yatai Kaikan, Kusakabe Folk Museum)
- Kyoto (Togetsu-kyō Bridge, Monkey Park, Bamboo Forest, Tenryū-ji, Kinkaku-ji, Ryōan-ji, Ginkakuji, Nanzenji, Yasaka-Jinja, Gion (just a short stroll), Kiyomizudera)
- Nara (Nara Park, Tōdai-ji, Kasuga Taisha, Kōfuku-ji)
- Koyasan (Kongobuji, Temple lodging, Danjō-garan, Oku-no-In)
- Osaka (Namba, Dotonbori)
- Hiroshima (Peace Memorial Park & Museum)
- Miyajima (Itsukushima, Mount Misen)
- Himeji (Castle, Koko-en)

From the first trip, what we have learned, is that we've seen too many temples and we wanted to get more feel of the current Japan and people's lifestyle. This time we will be having 15 and half of day for travelling over Japan (from beginning till the middle of November). So far I have chosen such destinations:
- Hakone (1 day trip from Tokyo, cruise, Sounzan Station, Open Air Museum, Onsen)
- Sendai - 3 day trip (1 day - Yamadera, 2 day - Zuihoden Mausoleum, Sendai City Museum, Sendai Castle, Osaki Hachimangu, Jozenji Street, 3 day - Matsushima)
- Kyoto - few days (1 day - Nishiki Market, Manga Museum, Fushimi Inari, Gion & Gion Corner)
- Nara (1 day trip from Kyoto - Horyuji, Heijo Palace, Nara Park - we want to see deers again :P)
- Kanazawa (1 day trip on the way from Tokyo to Kyoto - Kenrokuen Garden, Castle, Ozaki Shrine, Nomura Clan Samurai Home, maybe Ninjadera)
- Tokyo - few days (1 day - Ghibli Museum, Shinjuku Gyoen National Garden, Meiji Shrine, Harajuku/Shibuya)

So far we have circa planned 8 of 15,5 days. I was also thinking about giving Osaka some love. Maybe going to Ueno will be a good idea to see Ninja Museum there instead of Kanazawa's Ninjadera? Probably I would also like to see some more of Kyoto like the Nijo Castle, Imperial Palace, Otagi Nenbutsu-Ji. Is Yokohama worth going? Do you have any suggestions what else we could see and I should included in the itinerary? Or maybe you have any itinerary suggestions? For sure I will be grabbing a 14-day JR Pass, as it's price is similar to Kyoto - Sendai roundtrip by Shinkansen.

Thank you in advance for the help.

Best regards,
Sarachiel

For a small-town feel in a unique setting of mountainside living (no streets), I would definitely recommend the quaint little town of Onomichi (Hiroshima).

Hi!

What do you want in a ninja experience? We went to Ninjadera in Kanazawa and but we've not made it to Iga-Ueno yet. I really enjoyed ninjadera but my child was not feeling it. She wanted something a lot more participatory. If you're looking for an actual participatory ninja experience you might want to look at Koka or 48 Waterfalls down near Nabari. We went to the latter to do ninja training. It was fun, but really really hard and I was a terrible ninja. My child was far more successful.

If you like gardens, you could try to make it Takamatsu. Ritsuin is one of my favorites. You might also want to think about Matsumoto, the castle is fabulous and it would be a break from shrines and temples. My child really enjoyed Matsushima and the cruise in the bay.

I hope you enjoy your trip!

Thanks for the answers!

OP here (couldn't log in before). I was thinking intensively yesterday and came up with such itinerary for our trip:

day 0 - TOKYO: arrival in the morning, getting to hotel, Tokyo National Museum, Yanaka Cementary
day 1 - TOKYO: teamLab Borderless, Statue of Liberty (didn't see it first time), Giant Ghibli Clock, Tokyo Tower, Shiba Park, Zojoji Temple, Tokyo Skytree
day 2 - TOKYO: day trip to HAKONE, Togendai, Hakone Ropeway, Hakone Open Air Museum, Onsen
day 3 - SENDAI: Yamadera, strolling around Sendai
day 4 - SENDAI: Zuihoden Mausoleum, Sendai City Museum, Sendai Castle, Osaki Hachimangu, Jozenji Street
day 5 - SENDAI: day trip to MATSUSHIMA, Matsushima Bay, Zuiganji Temple, Fuukura Island, ship cruise, return in the evening to TOKYO
day 6 - KANAZAWA: morning train from Tokyo to Kanazawa, Kenrokuen Garden, Kanazawa Castle, Nomura Clan Samurai Home, Ninjadera, in the evening train to KYOTO
day 7 - KYOTO: Nishiki Market, Kyoto International Manga Museum, Fushimi Inari Shrine, Gion, Gion Corner
day 8 - KYOTO: day trip to NARA, Horyuji, Heijo Palace, Nara Park, Inari Shrine?
day 9 - KYOTO: day trip to UJI, Byodoin Temple, Ujigami Shrine, Manpukuji Shrine, The Tale of Genji Museum
day 10 - KYOTO: day trip from OSAKA, Osaka Castle, Shitenno-Ji Temple, Abeno Harukas, Shinsekai, Hozenji Yokocho, Dotonbori, Pokemon Center :P
day 11 - KYOTO: Nijo Castle, Kyoto Imperial Palace, Yokai Street, Arashiyama Station SPA, Saga-Toriimoto Preserved Street, Otagi Nenbutsu-Ji
day 12 - TOKYO: return to Tokyo from Kyoto, with mid stop in Nagoya/Yokohama? (pls suggestions :P)
day 13 - TOKYO: backup day (can be used anywhere or added a side trip - maybe you have any suggestions?)
day 14 - TOKYO: souvenir day, Akihabara, maybe Shibuya/Shinjuku
day 15 - TOKYO: Ghibli Museum, Shinjuku Gyoen National Garden, Yotsuya Suga Shrine, Meiji Shrine
day 16 - TOKYO: morning train to Narita, flying back home :(

What do you think about the plan shown above? Is it doable, not too fast paced? Or maybe you would make some changes in it? Thank you in advance for the help!