Japan

Tokyo:

• Tsukiji Fish Market:  We went at opening at 9 am (not the tuna auction which is at like 3 am).  Very interesting and you can go and eat in the stalls outside the market. 
• Robot Restaurant:  I know you already want to go there, so much fun :)
• Golden Gai:  A tiny alleyway of 4-5 seater bars.   They give you free snacks and you feel like you are in someones basement.   One of the most fun nights ever was spent here hopping around to different bars.  Some don't let foreigners in but you just move along to the next bar. 
• Other alleyways:  http://www.timeout.com/tokyo/restaurants/tokyo-alleyway-guide .  I went to Ebisu Yokocho, Nonbei Yokocho, Golden Gai, Omoide Yokocho, Daiichi Ichiba, Gado-shita, Suzunari Yokocho, Ameyoko, Shinbashi Yurakucho Gado-shita
• Karaoke:   Even if you're not a karaoke fan, do it.  We went twice to Karoake Kan, a chain (you will see their long blue lights  on buildings all over the city).  Some give you costumes.  We spent one night recruiting people off the street to do karaoke with us, so much fun. Its incredible to have Japanese businessmen belting out Ace of Base with you. 
• Shimokitazawa:  I stayed here for half my trip.  It's the Williamsburg of Tokyo and has so much to offer.  Lots of vintage stores (I had to pay $200 for an overweight suitcase on my return, all thanks to Shimokita).   Also, tons of teeny bars with live music.  I was traveling alone at this point and walked into so many and the crowd was always welcoming - you can walk in alone and they make you sit with them and give you free snacks.   I also saw some live music at a place called Basement Bar (main part of the club is called Three I think).  Mother's Ruin is an awesome bar and this was great Thai food : https://www.tripadvisor.com/ShowUserReviews-g1066455-d1693309-r342012262-Tit_chai_thaifood_restaurant-Setagaya_Tokyo_Tokyo_Prefecture_Kanto.html
• Koenji:  You'll be really hip for going here - its the new hipster up and coming area. 
• Shibuya:   Where the big crossing is.  So lively and fun, huge department stores (that you need to go into) and also small alleyways.  I stayed here half the trip and it was a really good choice.
• Harajuku/Yoyogi Park:  Go on a Sunday for people watching in the park. There are groups of the Japanese greasers that are fun to watch and lots of girls dressed in Harajuku style.     Go to the Meiji Shrine in this park to see beautiful sake barrels.  Takeshita-dori street to see all the crazy clothing stores and cool style.   
• Toy stores:  Wild, walk around them and see every toy you didn't think you needed but do. I became obsessed with this cartoon called Gudetama (stands for lazy egg) and bought so many Gudetama things
• Shinjuku:  The area of neon lights.  I spent a night taking photos here, its so Japan and so magical.   Some seedy areas, but so cool to see at night.  This is where Robot Restaurant is, so you can couple this what that night.  We also almost got beat up here (re: seedy area) but that was the only bad experience  we had with a Japanese person. 
• Animal cafes:  I went to a bunny cafe.  I am torn about whether it was humane, but so dang cute. 
• Akihabara:  Nerd heaven, def worth a trip.  Walk into a Pachinko parlor and arcades to see all the old games (Super Potato was an arcade with retro games).  Huge department stores full of nerd things.
• 7-11:  I went to one once a day, not only because they have public bathrooms but because there are more amazing snacks than you could imagine.  So many chip flavors and lots of Pocky sticks.   Also, we would have a daily 'Suntory' time, where we would buy a canned highball cocktail from 7-11 and walk around with it. 
• Don Quijote:  a glorious glorious department store.  They carry everything you need and don't need. 
• Park Hyatt New York Bar:  Lost in Translation filmed here, great views, cheesy lounge singers, def worth a trip

Hakone:  

This is a weekend getaway for many Tokyo residents.  Its an easy train ride away.  You should stay at a ryokan, a traditional Japanese guest house - you wear kimonos, sleep on tatami mats, get traditional dinner made in your room, the whole thing.   Many have onsen (public baths) in them.  We also took a shuttle to this onsen where you are outside in a natural hot spring in the mountains.  You have to go in naked (and they split up the men and the women), but its so relaxing you don't care.   They have lounge chairs outside overlooking the mountain for after the hot springs.   https://www.tripadvisor.com/Attraction_Review-g298171-d1554630-Reviews-Tenzan_Tohji_kyo-Hakone_machi_Ashigarashimo_gun_Kanagawa_Prefecture_Kanto.html 

Kyoto:  

I didn't love Kyoto as much as Tokyo, but worth a trip

• Golden Temple:  Beautiful picturesque building in the middle of a lake.  Screensaver worthy
• Fushimi Inari shrine:  Must do- thousands of red 'gates' that you walk through.  Make sure to do the hike all the way to the top (most people stop after the beginning).  There is a cute little 'rest stop' where you can have a beer and be totally alone in the mountains amid all the gates. 
• Bamboo forest:   A disappointment, but you gotta still see it. 
• Gion:  Geisha district, you might get lucky and see a real one.  Don't be fooled by the women that come here and pay to get dolled up as geishas - they are everywhere. 
• Nightlife:   Interesting nightlife here that revolves are teeny bars.  We went to Bar Dylan II ( a Bob Dylan themed bar) and a bar called Ups Club (hard to find, on second floor of a building sorta close to Dylan) where they play 'black music' (the Dylan bartender's words, not mine :) ).  There was also a Mexican themed bar that I can't remember the name but was cool.
• Pontocho:  a lovely old street, said Mexican bar is close by

Other:

• Bullet train: most fun sci-fi train ever.   You can see Mt.Fuji from train depending on where you're going. 
• Pocket wifi:   If you don't have service, you'll have a hard time.   Our AirBnBs gave us pocket wifis and they were so handy.   As amazing and helpful Japanese are, getting directions is extremely hard. 
• Food:  I am so bad at specific food recommendations, but I ate my face off with noodles and gyoza at the tiny little eateries there where you get tickets from a vending machine to get your food.  The only time we didn't get good food was some weird scallops at an izakaya and yakitori (chicken on a skewer).  
• Train stations in Tokyo:   Crazy huge.  A one point I screamed HELP HOW DO I EXIT because we walked everywhere and couldn't get out.  So packed and so Japan
• Kimono:  I bought a kimono there and wear it daily at home, definitely bring one back with you

Japanese people are the nicest ever, there's always something new to see, eat or buy, there's almost zero bad things to say about Japan.