A tour doesn't have to have a guide involved and can let you travel and stay more cheaply than a bespoke itinerary.

For instance, one of the cheapest ways of travelling between Tokyo and Kyoto is as part of a package deal
http://www.jtb-sunrisetours.jp/JTB.S...e=TYOOVJH2KAKE

This costs from 19,000yen each and includes return tickets on the Hikari bullet train as well as a night's modest accommodation in Kyoto.
What you can do is only avail yourself of the one night's lodging and choose to return on a later date so that you can spend 3 nights in Kyoto/Osaka (the other two nights at the hotel of your choice).

Osaka is only 30 minutes or so from Kyoto and costs about 500yen to get to by train.

This seems more sensible to me (and more cost effective) than getting an air pass between Tokyo and Kyoto/Osaka. It's also what I had in mind when I said that tours could be 'tweaked' to suit your needs.

Hi,

Yeah I wanted to spend New years in Tokyo.......So I was thinking to fly into NRT first....If I don't go to Hokkaido am I missing out a lot? If I skip hokkaido, I would just go to Osaka,Kyoto,Tokyo,Mt Fuji Hakone.Hmm if I wanted to go to hiroshima, how do I get there from Tokyo?

As you want to spend new Year @ Tokyo and Last 4 or 5 days @ Tokyo, I have been to Japan twice only so my rough planning as below.... (actually quiet a crazy packed schedule)

29 Dec Land @ Tokyo on NRT / HND flight, Straight to Hakone
Note: You may not able to catch the dinner provided by the onsen place if you fly NRT as first HKG --> NRT flight arrives at 1400 JPT, + train = arrive at 18:00

30 / 31 Dec AM Hakone / Mt Fuji
31 Dec --> 1 Jan Tokyo

2 Jan --> 8 Jan West Japan (Just fit the max time for JR pass, not opt flying cuz blackout period of Japan Air Pass)
2 Days Kyoto (Note to double check opening hours @ holiday)
1 Day Nara
1 Day Himeji + Kobe
1.5 Day Hiroshima
1.5 Day Osaka

Depends on your choice, few selections here

1. Overnight Sleeper train to Hokkaido
If you want to really experience Japan Rail Travel, Jump on Twilight Express (トワイライトエクスプレス) depart from Osaka mid-day, with your JR pass you should only need to pay for the room and heading Hokkaido

2. Shortcut to Hokkaido
If you want something quick and / or the sleeper train is not available that day, jump on a ITM --> CTS flight and travel to Sapporo, use the JR pass for your last leg of CTS to Sapporo Downtown

3. Spend more time @ West Japan and Skip Hokkaido
If you want to skip Hokkaido with more time @ West Japan, Book ITM --> HND on your preferred day

4. Spend more time @ Tokyo and Skip Hokkaido
If you want to skip Hokkaido with more time @ Tokyo, travel shikensen back to Tokyo on 8 Jan

9 Jan --> 12 Jan Hokkaido
13 Jan --> 15 Jan Tokyo

Thanks for that :) I will analyse the below and decide :) Also am I missing much if I don't go to Hokkaido and/or hiroshima?

I traveled to neither Hokkaido / Hiroshima, however http://www.japan-guide.com/ may be a good site for you to start

(Disclaim: http://www.japan-guide.com/ is my company's business partner)

Hi Chris,

Thanks. I will have a look.

Hokkaido's attractions are natural rather than historical, and I wouldn't recommend going there in midwinter unless you really like cold and snow or hope to visit one of the ski resorts or were able to time your visit for the Sapporo Snow Festival in February.

Hokkaido is at the same latitude as Minneapolis or Milwaukee and has winters to match. Save it for a summertime trip, when it will feel like a great refuge from the steamy summers of the other islands.

Hiroshima would take a lot less time to visit, and in addition to the atomic bomb-related sites, it has Miyajima and the Shukkeien to recommend it.

Thanks. Is Osaka, Kyoto a natural feel as well instead of historical?

Also which hot spring in near tokyo would you recommend? Hakone? Is there a private hot spring, i.e. only for a couple? Sorry new to this :)

Kyoto is all historical and cultural. But you can also see a lot of nature all around. There are a lot of hills/mini mountains all around Kyoto. In the 2nd World War, the American scholars was actually able to convince the military not to bomb the city. There many temples and shrines in the city. More than any other city in Japan.

Osaka is more a food place. There isnt really much "tourist" attraction there except the castle (not the best), kaiyukan (big aquarium - quite nice) and shopping. Lots and lots of shopping..Umeda and Dotombori area.

If you go to Hiroshima, you should definitely go to Miyajima.

Thanks guys for the info.

Will kyoto,tokyo,osaka,hiroshima,hokkaido have snow around Late dec to mid jan?

Hokkaido yes. The rest of the places, the snow dont usually stay on the ground long. Unless it is unseasonably cold..

When I lived in Tokyo, there was occasional winter snow, but it melted within a day or two. Daytime highs were almost always above freezing. The lowest temperature I ever experienced there was -4°C (about 25°C) at night.

The same is true in the rest of Japan south and west of Tokyo. I once took a student group to Japan in January, and we had highs of 5°C or more (about 40°F), except when we went to Takayama, which is in the foothills of the Japan Alps. In Takayama there was ankle-deep snow on the ground. Later, we had flurries in Kyoto, but the snow melted as soon as it hit the ground.