If this is your first visit to Japan, and if you are traveling alone, in a short amount of time, you might find the Kyoto area more rewarding based upon your wish list.
Kyoto is less than 2.5 hours by shinkansen from Tokyo, and provides a nice view of the countryside along the way. In Kyoto, there are more temples and museums than you will have time to see, and ryokan everywhere. The old Imperial Palace in Kyoto is much more rewarding, for there isn't really much you are allowed to see at the Imperial Palace in Tokyo. In the nearby city of Osaka, about 1 hour from Kyoto, you will find all of the same tall buildings, and night life of Tokyo, but with a friendlier and more convenient atmosphere. Plus the weather will be warmer than both Kyoto or Tokyo. In the mountains near Kyoto, you will find Shirakawa-go, a historic farmhouse town (though harder to get to), and Iga Ueno, the birthplace of Ninjas, is about 1 hour away. Onsen (hot springs) are common all over Japan, but are the least common in the Tokyo area.
As a resident of Tokyo, I have to say, if you are less familiar with Japan, I recommend putting off Tokyo for another time. Though, Tokyo is the biggest city in Japan, it is really just an enormous business center, with bitter salary men crushed into trains, and thousands of the most trend conscious in Japan wearing almost identical fashions. Resist the tendency to assume it has the most to offer because it is the world's largest megapolis. Some of the most remote parts of Japan have a lot to offer.
Also, if you don't need to fly into Narita, the most inconvenient airport in Japan, fly into Kansai (which is surprisingly uncrowded) or the new airport in Nagoya and save yourself a lot of time and frustration.
For a first time visitor, the Tokyo area can be overwhelming and takes too long to get around if you don't know exactly where you are going, plus people are less inclined to help you with directions. But, if you do stay in Tokyo, focus on Kamakura, for it is the closest match to Kyoto and easy to get around. Also, if you end up going to Kamakura, skip Asakusa. Though nice, it is highly over-rated and not worth the trouble to get there, and you will better in Kamakura. Meiji shrine, though different, is equally interesting, and is in the Shibuya area. Akihabara (the electric town) is usually interesting for first time visitors. And though I like Shinjuku, it is probably the least entertaining for tourists.
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