When visiting Japan, I highly recommend the J-rail pass! For a couple hundred dollars, you can take the bullet train for 7 days. During my week, I went from Tokyo to Nagano to Kyoto. It was efficient and FAST! The train stations were a little confusing in Tokyo, but other than that, it was a breeze to get around. While in Tokyo, we made our rounds to all the quirky cafes: Robot Cafe, Kawaii Monster Cafe, Hello Kitty Cafe, and the Owl Cafe. We stayed in Shibuya in the middle of everything and air bnb'ed our accommodations.
Japan has a magic and romance to it. Even in the crowded urban areas, the air feels dreamy. We spent all day walking around the Fushimi Inari Torii gates. These red shrines are a network of 10,000 red arches that extend through the forrest behind the main buildings. Although fairly touristy, the higher you go, the less crowded it is. We then explored Higashiyama District, which is a really well preserved historic part of the city. There are tons of small shops, cafes and restaurants. We spent the evening meandering through the quaint little alleyways and stopping for Hello Kitty pancakes ^__^
No trip to Japan is complete without going north to the snow monkey park! I spent all day there and then at night, stayed in historic Shibu Onsen. I dressed up in the complimentary kimono at the ryokan (traditional Japanese hotel) and made my rounds to the 9 onsens (bath houses) along the main road. The onsesn are nude and separated by men's and women's. If you are going there for a romantic get away, it's best to book a hotel with your own private onsen as opposed to the public ones that I did. The hotel included a traditional Japanese breakfast and dinner. You can't go wrong with this experience. I got a lot of my information from this site when deciding where to book: http://www.yudanaka-shibuonsen.com/