Kyoto is wonderful, as long as you aren't arrogant and make some attempt to communicate in Japanese, people will love you (in general). Also, the signs for public transport are in English so it's easy to get around. Kyoto is packed with tourist sites of the historical variety which is great if you like history. Personal favorites are Ginkaku-ji and Honno-ji, the latter being where Oda Nobunaga died. Also, Nintendo HQ is about 11-12 blocks directly south of the major train station. It's a great city to build a trip around, because it's smaller than Tokyo so there isn't quite as much to experience, and it's extremely friendly to foreigners. I can't say enough about how nice the people are. It's also right next to Osaka which is the second largest city in the country.
For food, you can't go wrong with Okonomiyaki, and Katatori-kun is spot on with the prices. If you really want to treat yourself, go to a Korean BBQ place. It's pretty expensive, I think around $30 a person, but really good. If you want to travel, the JR Rail Pass is absolutely what you want to do. Taking the bullet train is crazy expensive otherwise. Just be sure to purchase the pass before you go because it's only available to foreigners.
As for other sights, I've only toured the southern region but Miyajima is gorgeous though probably a tad pricey, Nara is really fun to visit because of the older temples and the deer. Kinosaki-onsen makes a great mid-trip relaxation spot just be sure to do some research beforehand on proper customs of Japanese public baths because they take bathing very seriously and you don't want to be "that guy".
If manga and gaming are your thing, also be sure to visit a chain called "Book-off" because they've got a great selection for pretty cheap. Gaming is more expensive than in America, but manga is dirt cheap. Book-off sells high-quality secondhand manga volumes for only 105 yen and the new stuff is only 250-450 yen. I bought the entire series of Urusei Yatsura (32 volumes) for less than Pokemon Black 2, and the game was tax-free.
For food, you can't go wrong with Okonomiyaki, and Katatori-kun is spot on with the prices. If you really want to treat yourself, go to a Korean BBQ place. It's pretty expensive, I think around $30 a person, but really good. If you want to travel, the JR Rail Pass is absolutely what you want to do. Taking the bullet train is crazy expensive otherwise. Just be sure to purchase the pass before you go because it's only available to foreigners.
As for other sights, I've only toured the southern region but Miyajima is gorgeous though probably a tad pricey, Nara is really fun to visit because of the older temples and the deer. Kinosaki-onsen makes a great mid-trip relaxation spot just be sure to do some research beforehand on proper customs of Japanese public baths because they take bathing very seriously and you don't want to be "that guy".
If manga and gaming are your thing, also be sure to visit a chain called "Book-off" because they've got a great selection for pretty cheap. Gaming is more expensive than in America, but manga is dirt cheap. Book-off sells high-quality secondhand manga volumes for only 105 yen and the new stuff is only 250-450 yen. I bought the entire series of Urusei Yatsura (32 volumes) for less than Pokemon Black 2, and the game was tax-free.