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Yet another 1st time trip to Japan - 3 weeks - advice much appreciated.

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Hi
Another first time trip to Japan. Also it's likely to be the only one too so I want to make the very most of it. There are so many places in the world we want to visit and we've been lucky enough to see many so far but realistically it's likely that we won't be getting back to Japan. I've wanted to visit for a while now and have been inspired by some of the fabulous trip reports on here. As Kavey said the opportunity to observe a culture and set of traditions wholly alien to our own is a huge attraction for this trip.

We want to see the best that Japan has to offer but also want to fit in some off the beaten track experiences - and I know these are conflicting aspirations. We love history and getting outdoors but love cities just as much, but are not so into the onsen experience, I think. It will be a mix of expensive and cheap. A top end restaurant one night - supermarket takeout the next, same with hotels.

The trip is going to be 2015 and October/November seems to be the best time to visit.

My first draft itinery came to 35 nights and I know we Brits get great holidays but even that's too many. So I had to drop Sapporo and Hokkaido and northern Honshu, DisneySea, Nikko, Naoshima, snow monkeys and Fukuoaka as well as cutting the amount of time spent in Tokyo and Kyoto so we have just 4 nights in each city. I've kept 2 night in Kanazawa, Hiroshima and Yakushima though.

So here's my first proper draft itinerary:

Emirates flight leaving Manchester on a Friday evening. DP wants to stop somewhere on the way (I'd prefer not to but it's a compromise I think I need to make) so Dubai looks to be the best option. Also it's not a place we'd ever go otherwise I think.
Night 1 - on plane
Night 2 - arrive early morning in Dubai
Night 3 - Dubai
Night 4 - plane leaves Dubai 8:15 arrives Tokyo Haneda 23:00. We could get a flight the night before that arrives very early morning in Tokyo on day 4. Thoughts?
Night 5 - Tokyo - to max the chances of seeing Fuji without cloud we'd do Hakone in a day trip depending on the weather and we have no huge desire to stay for the onsen.
Night 6 - Tokyo
Night 7 - Tokyo
Night 8 - Debating whether to hire a car and drive for the next few days. We love driving holidays and the freedom/flexibility it brings over trains. Also we get to drive on the same side of the road as home. Overnight in Matsumoto? Mrwunrfl suggests that Matsumoto castle can be seen without the need to stay overnight.
Night 9 - Alpine route. Overnight in Kanazawa
Night 10 - Kanazawa
Night 11 - Overnight in Takayama
Night 12 - We want to hike between Magome and Tsumago so overnight in Tsumago?
Night 13 - drop car off during the day somewhere convenient and get train to Kyoto.
Night 14 - Kyoto
Night 15 - Kyoto
Night 16 - Kyoto
Night 17 - Nara
Night 18 - Hiroshima - having seen Himeji Castle on the way, which will be unwrapped by then.
Night 19 - Hiroshima
Night 20 - Miyajima
Night 21 - Yakushima - the hiking here looks so good.
Night 22 - Yakushima
Night 23 - leaving Yakushima lunchtime to get to Osaka late evening for a 23:40 flight home. Arrives home on the Sunday morning.

Am sure I will have lots more questions as time goes on but first it would be great to get your thoughts on the draft itinary. Also:
Is getting in to Tokyo at 23:00 a really bad idea?
We'd love to drive so is the section from between Tokyo and Kyoto a good chance to do this?
I'd really appreciate advice on how best to work those days - for example, could we get to Kyoto without overnighting in Tsumago? Also I'm not even sure if I have them in the most logical order.
Should we take a night off Hiroshima and add it to Kyoto?
Is mrwunrfl right about not needing to sleep in Matsumoto?

I know I've got lots of reading on www.japan-guide.com to do.

Many thanks, Tim

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