Almost 3 weeks in Japan, having trouble figuring out how long to book stays in each city

My partner (27F) and I (26M) will be spending 19 full days in Japan in October (flight just after midnight in NY Oct 5th, leaving evening of Oct 25th). We have an idea of where we want to go, but not really how long to stay at each place. We generally want to see the main attractions of each major area, as well as a few extra things that might appeal more to our particular interests (namely Pokemon and anime/games in general, as well as car enthusiast attractions). I know the next step is to book hotels, especially as the trip is almost 6 weeks away, but I've never had to book so many separate hotels for a single trip so I'm worried we'll be cutting some experiences short by not having a clear idea of what to do before we book stays. we're also trying to minimize changing hotels as much as possible to avoid the annoying of bringing bags with us as well as having fewer booking itineraries if possible.

This is a very rough general itinerary of the main hubs where I want to book hotels and the day trips we'd like to make from them:

Tokyo (part 1)

We're flying into Tokyo so makes sense to start there. We'd also stay there the longest so it makes sense to break it up into two separate stays, preferably with different emphasis on location and what we do. I think the first stay in Tokyo should be focused more on experiences with few souvenirs if possible, so we don't fill up our bags right from the beginning. I still have to plot out which districts we'd want to stay in or visit between the first and second visits to the city, but I also know the first leg of Tokyo is the lowest risk to "under-"book" since we'll be back toward the end of the trip.

Day trips from Tokyo:

  • Yokohama: Chinatown and the ramen museum are cool to see, plus we want to check out some of the Nissan related locations like the Nissan Heritage Museum (even if it's out of the way of central Yokohama)
  • Kamakura: Lots of cool shrines and statues, plus we can make it a combined day trip with Enoshima
  • Motegi: Fairly far out from Tokyo with no direct train lines, though we can either take rail up to Utsunomiya and rent a car from there, or just rent in Tokyo and make the drive up ourselves. The real attraction here is the Honda Collection Hall, as well as the raceway nearby. The Collection Hall is probably the car related sight we'd want to see the most on the trip, which is why we'd go pretty out of our way to hit this up
  • Mount Takao: This is more of a "if we're in the mood" kind of deal since it's more of a hike than anything else, but it seemed cool to me and lots of people suggested it on this sub

Hakone

We really want to spend some time in an ryokan together, so this was high on our list. We'd likely spend two full nights here, which lets us complete the full Hakone loop at our pace as well as possibly try a JDM car experience with Fun2Drive with iconic cars and roads.

"Day trip" from Hakone:

  • Nagoya: We'd either visit Nagoya on the way from Hakone to Kyoto if the timing made sense, or if not we'd make a day trip from Kyoto later. The main appeal here again is the assortment of Toyota-related museums here, particularly the general automobile muself and the Commemorative Museum of Industry and Technology. There's also the train museum if we find we have time for that, but my partner isn't super interested so if there any other things that are cool to see in Nagoya, suggestions are welcome!

Kyoto

There's a lot in Kyoto that you can't really experience at the other places since it's still so historically significant, but I'd admittedly have to do more research as to what to check out while there. Philosopher's Path, Kiyomizudera, and Fushimi Inari stand out at first glance, among others. Also don't have a clear idea on day trips we'd make from here (suggestions are helpful!), but I also know that Osaka and Kyoto being so close make it such that most destinations you can visit from one can also be easily reached from the other. Funny enough, the Henn Na dinosaur hotel caught our eye as a place to stay (my partner loves dinosaurs lol), but it's a bit pricey to stay at for more than a few days, so we'd either have to have a relatively short stay in Kyoto to justify booking that hotel, skip the hotel altogether, or stay at two different places here.

Osaka

A city I see many suggest to skip, but with how long this trip is as well as many of the cool things I see of Osaka, that is a suggestion I'm willing to ignore. Particularly of note to me are Dotonbori, Shinsekai, Shinsaibashi, Den Den Town, and even Amerikamura. Will also have to do a bit more research on other noteworthy spots here. This is also a great place to make a bunch of day trips from, though if our accommodations in Kyoto are a good bit cheaper then it may make more sense to have Kyoto be our home camp for those trips.

Day trips from Osaka:

  • Nara: Self-explanatory. Can take this trip from Kyoto if timing works better there
  • Kobe: I've heard this makes a great afternoon day trip, especially around lunch time, so considering making this trip on the way back from Himeji instead?
  • Himeji: I considered going to Himeji on the way to or from Hiroshima but it probably makes more sense to make this trip standalone from Osaka, both so we can go early and try to beat the late morning/afternoon crowds and so we don't have to deal with finding a place to stow luggage on the way to Hiroshima

Hiroshima

Will do the typical sights here, including the peace park and museum. I'm also curious about the differences between Kansai and Hiroshima-style okonomiyaki, so I'd like to check out out Okonomi-mura as well. There is also the Mazda museum which is interesting to us, but it's by reservation-only and I believe tours are only conducted fully in Japanese, so we'd have to see if we can justify that. Not sure if we'll want to spend 2 nights here or just 1, as it sounds like we can see everything we'd want to see in one full day, but two days gives us a better chance of heading to Miyajima early in the morning to beat other tourist crouds.

Day trip from Hiroshima:

  • Miyajima Island: The floating torii gate at Itsukushima is the primary attraction here, but it would also be nice to just enjoy nature and a bit of a hike on the way up (or down) Mount Misen. I know we'd have to take a fairly early ferry to Miyajima to have any sense of peace or reasonable lines there.

Tokyo (part 2)

The latter half of Tokyo would most likely consist less of travel but way more of just buying things that we wouldn't want to miss out on while we're here, like figures and other merch, souvenirs, and gifts for back home. This would probably mainly include Shinjuku, Akihabara, and Shibuya. Any ticketed events (like Ghibli Museum or Pokemon Cafe) would try to be booked on this leg if missed the first time around.

Sorry for the super long post, but just wanted to share a general sense of what we want to accomplish and enjoy while in Japan. We would very much appreciate suggestions on how long each leg of the trip should be to reasonably travel without feeling overwhelmed, absorb as much as we can, and not miss any particular sights or events due to places being closed on certain days of the week. Feel free to leave feedback and questions and I'll try to answer accordingly.

by KSoMA