Two weeks is a tough amount of time to spend in Japan.
Ideally you'd be able to throw a couple more days in there so that you can see a few more places than just the main tourist cities.
Tokyo is going to demand at least one week just to get around to the different hot spots and beautiful areas.
Kyoto is incredible. there is no other way to describe it. and it will also probably demand a week of your time. but you could shorten it by a few days if you wish to see more.
if you wish to experience more of Kansai (which you can do if you purchase a one-week shinkansen pass), you should try to see Nara, Himeji, Miya Jima (although the main temple there was recently, so you could skip it) and Hiroshima.
Nara is an ancient capital, and its filled with amazing temples (including Todai-ji, which is the biggest). its a serious must.
Himeji is the home of Himeji-jo (Shogun Tokugawa's own castle) which is the most incredible ancient japanese castle you will ever see... (and i owe my own experience there to the tfp, because i asked almost the exact same question two years ago)
Miya Jima is a tiny island with an important temple... but it also has the floating Torii (that red gate 'floating' in the middle of the water that you see in the tourist pictures. but as i said, the temple was ruined by either a typhoon or a ship (i forget which) recently, so this could dampen the experience a bit... they also have the most incredible oyster trade there.
Hiroshima is a strong possibility for obvious reasons.
I never got to Osaka, so i can't say if its too similar to Tokyo.
as for accomodation... in Tokyo i recommend Kimi Ryokan (its the most obvious choice for westerns who've read the lonely planet... but don't let that distract you... it really is a great, clean, private place which is very affordable). its in Ikebukero, on the Yamanote line (for one-weeks worth its the only public transport you'll need to worry about, except if you wish to get to roppongi), and its fairly easy to get to.
i stayed in a much smaller ryokan in kyoto. and that was lovely too, but since it was a family run place, they did have a curfew, so that might be something to remember. Kyoto has hundreds of places like that. the city itself is fairly manageable since it has a manageable bus system and a subway.
safety in the ryokans (and indeed Japan as a whole - by far the safest place i've ever experienced) i stayed in was not an issue. but to be on the safe side, i'd make sure your laptop was at least out of view in your suitcase (locked) when you weren't there.
i'd love to read other opinions about Osaka.
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Ohayo!!!
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