2nd time in Japan - early January

First off, just a quick geography check: Osaka/Kyoto/Kobe are west of Tokyo, not south of it.

Next: are you aware of what the weather's like in January? It's generally pretty cold, even in the big cities. Places up in the mountains, or way up north in Hokkaido, are going to be notably cold, probably with lots of snow. Is that what you're looking for? Snow helps some activities, and precludes others. I wouldn't go to Hokkaido in winter unless you want to ski, or see lots of snow.

Otherwise, on your specific enquiries: Hakone will be cold in January. I'm not sure it's the best season for Hakone, though there are lots of onsen up there where you can warm up. If it's not snowy, you could still hike around, if only to keep warm! You will of course only see Fuji if you're lucky with the weather.

If you haven't been, Kamakura's a great day-trip from Tokyo. Lots to see (more than you can fit into just one day, actually), and some really lovely shortish hikes, where you'll see Fuji (if you're lucky with the weather). Parts of Kamakura can get very busy, so go early! And stop off in Yokohama for the evening on the way back.

Nikko is much better done as a trip with a night or two there, than as a day-trip from Tokyo. There are lots of onsen around there too, should you want to indulge there. Inner Nikko is rather beautiful.

Kanazawa is really cool, I am less keen on Takayama. Shirakawa-go is very, very touristy, but I'm sure the traditional houses there look rather lovely in the snow. Expect lots of tropical tourists going berserk because they've never seen snow before though.

There's lots and lots of cool stuff in Japan between Tokyo and Kyoto, particularly if you take the northern route through Kanazawa. You could stop off in Nagano in the mountains, perhaps somewhere in Fukui, then in Shiga (Lake Biwa is full of birds in the winter, if that interests you). Plenty to fill 16 days. Just note that places in the mountains and along the Sea of Japan are likely to be snowy, and everywhere is going to be fairly chilly.

Kanazawa is really cool, I am less keen on Takayama. Shirakawa-go is very, very touristy, but I'm sure the traditional houses there look rather lovely in the snow. Expect lots of tropical tourists going berserk because they've never seen snow before though.>

I visited Takayama and Shirakawa-go in the winter of 2005 and had a great time. These places didn't strike me as being any more or less "touristy" (whatever that means exactly) than many of the numerous other places I've visited in Japan over the past 30 years, but it's possible the recent boom in foreign tourists may have changed things somewhat. Certainly when I visited from Taiwan during the Lunar New Year the area wasn't overrun by tourists (Japanese or otherwise). IMHO, the best time to visit Shirakawa-go is when the gassho-zukuri houses there are covered in snow (and I didn't encounter anyone losing their marbles over all the white stuff!). Walking through the snow in the Higashiyama temple town area in Takayama was also very atmospheric, and the night illumination at the Hida Folk Village was pretty cool (no pun intended) as well.

If you do go to Takayama, you might want to make a day trip to Furukawa, only 15 minutes away by train, where there is a small but atmospheric old town and a lot fewer visitors than in Takayama.

We should be fine with a little cold. Especially the type of weather I been reading about in Tokyo.

@Giora Thank you for idea to do Kamakura and Yokohama in a single day trip. I have never been to both of those places before. We will definitely to do that!

Kanazawa seems to be the most direct destination from Tokyo (via Hokuriku-Shinkansen). I guess I should be able to go to Shirakawa-go from there. Or go to Fukui. Are there any good onsen spots in either of those or other place between Kanazawa and Osaka? We want to stay at least a day or two in ryokan.

I looked at the ways of getting to Takayama, but it takes at least 5 hours. But at least there is a night bus from Tokyo to Takayama. The trip from there to Osaka also seems lengthly, unless I will stop over for a day or two in Nagoya (I guess Nagoya has few interesting museum, but I am not sure what else it has)?

Yokohama's interesting enough to merit a day-trip in its own right, but if you don't have time, visiting it on the way back from Kamakura is also a good option. I personally really like wandering around Yokohama in the evening.

On onsen: there are onsen towns all over Japan. There are several onsen towns in Nagano which are near the Hokuriku Shinkansen. I really liked Bessho-Onsen, for example. Japan-guide has a few more suggestions. Otherwise, there are some onsen towns in southern Ishikawa Prefecture, and also up in the mountains around Hakusan. There are probable onsen in Fukui as well.

The city of Nagoya itself is largely modern, but has a nice castle, a couple of great museums, and a few sights and places of interest scattered around. The surrounding region has lots and lots to see. Inuyama, with a fabulous castle, teahouse, and my favourite museum in Japan. Seto, an interesting little pottery town with perhaps the finest pottery museum in the country. Okazaki, hometown of Tokugawa Ieyasu, with lots of temples, shrines, and historic sights. The Kiso Three Rivers, with some lovely views. Gifu, which is an interesting city with a nice history. If you do go, you'll find something for your tastes in the Nagoya region.

I also like Nagoya simply for being a large urban center with far fewer tourists than Tokyo or Osaka. It's a good place to see what modern, urban Japanese life is about.

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