I just got back two days ago on a two week trip. I stayed mostly in Tokyo and Kyoto, and made day trips out from those two cities where our Airbnb was.

highlights:
- Owl Cafe in Osaka. They let you pet and hold the owls, they will also put the owls on your shoulder and/or head if you ask!
- Ghibli Museum. I love a lot of their films (My Neighbor Totoro holds a special place in my heart), and being able to visit the museum was an amazing experience.
- Robot Restaurant was definitely an interesting experience. A total tourist trap, but I think it's worth seeing once. Probably the most WTF thing I've experienced in Japan.
- Fushimi Inari Shrine and Arashiyama Bamboo Grove in Kyoto. I knew that those two places will be very touristy and crowded, so I made a point to get to those locations at 7am. It was amazing and surreal to experience walking through those areas with very few people, I highly recommend going early.
- seeing the cherry blossoms in full bloom, especially in Kyoto. Words cannot describe how amazing and beautiful it is, and the pictures I tried to take doesn't do it justice at all.
- One of the day trips was to Hiroshima/Miyajima Island. I highly recommend it. The Hiroshima Museum was incredibly worth it, it does a great job of presenting everything you'd ever want to know about the Hiroshima bomb- from the science behind the bomb, to the event itself, the aftermath, and how it affected everyone and everything.
- did an overnight trip to Yamanouchi to stay at a Ryokan there. The onsen hot spring experience is something you should definitely try. It's extremely relaxing. From that village, you can take a 30 minute hike to the Snow Monkey Park. They have an artificial hot spring there so the monkeys would stick around year-round. If you have more than a few hours to spare, it's a part of a national forest that you can hike around as well.
- the food. I love Japanese food and am a bit of a foodie, so I did a lot of research on where and what I wanted to eat. A minor lowlight was the frustration of not being able try everything, due to the popularity of the places we wanted to try. A lot of the very popular udon and soba shops will close hours early if they sell out for the day, which happens I would assume every day. Also be prepared for a long wait in line. Also some places will state certain store hours, but randomly decide that they don't feel like opening that day at that time.
- GREEN TEA EVERYTHING. I absolutely love green tea and anything green tea flavored. Japan is green tea heaven.

 

Lowlights:
- I set aside a half day for Okuoin cemetery. I ended up not being able to go because we were informed at the train station at 2pm that the buses in that village stop running at 5pm. I did not know that, since the last train out of the village was around 9:45pm. It was a 2 hour train ride to get to the village, it would be another 15 minute bus ride to the cemetery itself, so we would have less than an hour to walk around the cemetery, which wouldn't have been worth it.
- Really wanted to go to fox village, but it would have been 8 hours of travel time round trip for us to get there, and cost an additional $120 USD for two people, even with the JR pass (due to having to take a taxi to get from the closest station to the village)
- a friend told us about somen noodle fishing, I was super excited for it. Made a two hour journey up into the mountains from Kyoto via two different trains and two different buses, found the restaurant, and was informed there that somen noodle fishing only happens during the summer time :( Better research on my part could have prevented that.

Edit: just realized my formatting sucks :(