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Advice on where to stay in Kyoto--and some other questions about May trip

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Hello everyone, I've been perusing old threads and finding wonderful and incredibly helpful information here but have a question that doesn't seem to be addressed in other threads--specifically, whether it is reasonable to plan to stay in Arashiyama during the 5 or 6 days we will be in Kyoto. We are a couple who love to stay in independent apartments when we travel, and we have found some appealing candidates in Kyoto on VRBO--but we are torn about Arashiyama vs. Gion, or elsewhere. We don't want to spend a lot of extra time on trains/buses, but we do like to be out of the most touristy areas. The Arashiyama machiya looks lovely, but I don't want to doom us to lots of schlepping.

Some other info about our trip: this is our first time in Japan (so excited!!), and we will be there for 13 nights (May 6 through 19), flying in and out of Narita. We are planning to spend 4 or 5 nights in Tokyo and 5 or 6 in Kyoto, with maybe a few nights elsewhere (Takayama/Shirakawa-go or the Izu Peninsula?). We will probably stay in a hotel in Tokyo and are hoping for a ryokan experience for a night or two of our trip. We love good food, being active (would love to rent bikes in Kyoto), spending time in museums/historic sites, exploring markets (but not shopping per se), getting off the beaten track.

Given our interests, would it be insane to just plan to stay in Tokyo and Kyoto and not spend a few days elsewhere? Of course I hope that this will be the first of many trips to Japan, but you never know--we live in Maryland and it's a pretty long trip, and my fiance has a long list of many other countries he is hoping to visit! So I don't want to miss the chance to experience a different (and more rural/remote) part of Japan.

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