Dear Maria, I totally empathise with you planning your first trip to Japan and getting things organised. I also have been planning my first trip to Japan next April since June and can completely understand what you're going through. I only have 14 days including 2 international travel days so I'm only left with 12 sightseeing/internal travel in Japan.
There is so much to do and see and never enough time. Initially I wanted to do Tokyo, Kanazawa, Takayama, Mt Fuji and Hakone, Hiroshima, Osaka, Kyoto, Nara, and Koyasan, experience an onsen a and a stay in a ryokan. I'm not a big fan of theme parks but this trip is not just for me but for my family too so everyone gets to do something that they really want. But I decided to focus on the most the important places that me and my family want to visit e.g. Tokyo with a visit to Disney Sea and Studio Ghibli, Kyoto, Universal Studios in Osaka, Hiroshima and Miyajima, and Hakone (perhaps with an overnight stay in a ryokan)?
The first thing I did was plan the route of travel and that took some time but with the help of hyperdia google maps, and this great site and forum, I got to understand the distances and travel time between them and I finally sorted it out, so for us it will be Tokyo- Hakone- Hiroshima- Osaka- Kyoto.
Next step was finding hotels in the dates I allocated to each city...and yes it was frustrating trying to find availability in a specific hotel/ryokan on the date that I wanted, but I noticed that some don't open their availability that early. Some will start releasing it day by day from beginning of October for April, so I'm checking their websites daily. Booking a few with free cancellation until I decide is what I did until I figure it all out. The most overwhelming thing for me was deciding on a hotel in Tokyo, but thankfully I finally did and that was a great relief!
So my advice is sit with your family or whoever you are traveling with, decide on what your priorities for this trip are and what things you want to do exactly in each location.
In regards accommodation, you don't have to stay in a ryokan in every city.. I realised earlier on in the search for accommodation that there are most ryokans in Kyoto are already fully booked for this period, so for the experience I am looking at an overnight in a ryokan in the Hakone area. If you are planning on staying in Miyajima then perhaps check ryokans there or on the shores of Hiroshima facing Miyajima (the area of Hatsukaichi for example).
Don't forget while planning to take the travel time from one city to another into consideration, e.g. Koyasan to Miyajima persay... that's like 5-6 hours including the ferry from Hiroshima, so that's like a day wasted just on travel. So maybe plan your route better. Miyajima is only 160min from Osaka (including the ferry time).
Like others said check flight times to Okinawa and if they suit your plan and budget then include it by all means.
Once you have sorted the big things such as accommodation and travel dates, then the planning of day to day activities begins, and things like ordering a 7 day JRP, tickets to Studio Ghibli (which I have to wait until January to order them on JTB website), Disney Sea and USJ tickets, the Suica cards, the pocket wi-fi, etc... (these are all early next year's tasks). But I always have plan A, B and C in case things don't happen according to my first wishes
I have settled in the end that the more I focus on one place the better, and there will always be another time to visit Japan and see the areas that I couldn't fit in my upcoming trip.
So take a deep breath and relax... you can't plan properly when you're stressed. Perhaps enjoy a cup of green tea while planning. That should get you in a better mood. So best of luck planning and enjoying your trip next year.
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