13 day Japan itinerary and questions

I am putting together a rough itinerary for a trip my girlfriend and I are taking in November. We’ve established we will visit Tokyo and Kyoto with some days in the mountains in Nikko and Hakone. I am still somewhat unsure about visiting both Nikko and Hakone given the length of our trip, so I am looking for some feedback. Assuming we do both, this would be our itinerary:

Day 1

  • Arrive Narita airport at approximately noon (traveling from Seoul after staying there, so no jet lag)
  • Rent car and drive to Nikko (see question at bottom)
  • Lodging in Nikko for 2 night stay (half board at Ryokan)
  • Onsen and dinner

Day 2

  • Full day in Nikko area
  • Morning: Toshogu Shrine and vicinity, then drive to Lake Chūzenji and Ryuzu Cascades,  Kegon Falls, perhaps a hike near Lake Chuzenji.
  • Enjoy the onsen and dinner at our Ryokan.

Day 3

  • Checkout from Ryokan in Nikko after breakfast.
  • Spend morning/early afternoon in Nikko area then make our way to Tokyo.
  • Drive to hotel in Akasaka and drop luggage, then return the car somewhere in the city.
  • Spend remainder of the afternoon/evening at Shinjuku Gyoen and Shinjuku area.

Day 4

  • Full day in Tokyo
  • Morning: Meji Jingu Gyoen, Meiji Jingu Gaien
  • After lunch: Shibuya and National Art Center.
  • Dinner near Shibuya or Asakasa

Day 5

  • Full day in Tokyo
  • Morning: Senso-ji early then Tokyo National Museum and Ueno Park
  • Lunch in Asakusa and sightseeing in the area
  • Evening: Akihabara sightseeing and dinner

Day 6

  • Full day in Tokyo
  • Visit Imperial Palace and gardens then visit the Ginza area for lunch and light shopping.
  • Afternoon: Teamlabs Borderless
  • Dinner in the Roppongi area or closer to hotel in Akasaka

Day 7

  • Check out from hotel in Tokyo
  • (Maybe) Ghibli Museum (this is the only day it is open during our time in Tokyo)
  • Take train to Hakone
  • Loding in Hakone (Gora) for 2 nights (half board at Ryokan)

Onsen

Day 8

  • Full day in Hakone
  • Open Air Museum
  • Visit Lake Ashi, take a pirate ship ride, find somewhere to view Mount Fuji, take the Ropeway back to Gora
  • Dinner and onsen at the ryokan

Day 9

  • Check out from Hakone
  • Train to Kyoto
  • Check in to hotel in Kyoto (4 nights)
  • Time permitting: Heian Jingu Shrine, Nanzen-ji and other shrines in Sakyo ward

Day 10

  • Full day in Kyoto area
  •  Fushimi Inari, Tōfuku-ji, Kiyomizu-dera, other spots not reached due to time from previous day.

Day 11

  • Full day in Kyoto
  • Day trip to Nara or Kanazawa

Day 12

  • Full day in Kyoto
  • Tenryu-ji Temple, Arashiyama Bamboo Forest, Kokedera

Day 13

  • Check out from hotel in Kyoto
  • Take train to Kanasai Airport to fly to USA

Is it too much to squeeze Nikko and Hakone into this trip? Or should we just pick one over the other? If we only pick one, I am leaning towards Hakone (largely for less difficulty with getting there..also see next question). If we don’t go to Nikko, we would go to Hakone during our first days in Japan, followed by Tokyo, then Kyoto. While this is backtracking, it would allow us to be in Tokyo when we could visit the Ghibli Museum since it is closed for part of our days in Japan (if we can get tickets). Otherwise we wouldn't backtrack, Our itinerary in Tokyo and Kyoto would remain largely the same however it would allow for a third night in Hakone and a fifth night in Tokyo. An extra day in Hakone could be spent going up towards Fuji Five Lakes and an extra day in Tokyo would allow us to spread our activities out or add more activities. Plus it would give us more opportunities to visit the Ghibli Museum since that seems to be one of the more difficult things to do.

If we do go to Nikko, we are leaning towards renting a car upon arriving at Narita. We felt this would offer us the most flexibility to see the area without dealing with crowded trains. We would then return the car in Tokyo two days later and use trains the remainder of the trip. Is renting a car worth it for the convenience? How difficult would it be to return the car somewhere in Tokyo after dropping luggage off at the hotel in Akasaka? We are open to other transportation options for Nikko if rental car is too troublesome. We’d also consider not staying in Nikko and just going there as a day trip from Tokyo instead if the highlights can be seen in a day.

Are there any days where we are doing too much or too little in one day? I tried to arrange things in Tokyo and Kyoto to be in one area each day as best as I could.

Any other advice/suggestions are welcome!

by Skyguy414