Tokyo

• It's not easy to get to, but if you like bonsai, you MUST visit Shunkaen Bonsai Museum(map)
• Areas you should visit:
  • Ginza (fancy area with expensive shops, Ginza Six mall is nice with a beautiful Tsutaya bookstore on floor 6)
  • Shibuya (watch Shibuya Crossing from a free lounge on floor 12 of Shibuya Scramble Square mall, hachiko statue, crazy fashion in Shibuya 109)
  • Akihabara (no intro needed, walk around Yodobashi Camera, Shogun burger has wagyu burgers)
  • Harajuku (crazy fashion worn by young people, hip area, car fanatics might like the Liberty Walk store (map))
  • Shinjuku (busiest train station in the world, nightlife and red light district is here, Tokyo Metropolitan Government Office has a free observation deck)
  • Daikanyama (Brooklyn of Tokyo, probably the neighborhood I would want to live in, has the amazing Daikanyama Tsutaya bookshop (ranked among most beautiful in the world, also has a coworking space), log road daikanyama is cool, good brunch at Clover's)
• Ippodo Tea Tokyo is not at the same level as their Kyoto store, but it's still worth visiting (map)
• I do not exaggerate when I say this Starbucks next to the imperial palace (map) is the nicest Starbucks I have ever seen. Worth a visit, although the line can be long.
• If you want to take many photos of shinkansen, go to Tokyo station and buy the $1 ticket to the shinkansen platform. Explanation here
• Tokyo Sky Tree (map) has a great observation deck and large mall at the base
• Tokyo has the most michelin starred restaurants in the world, including some of the cheapest (see this list). Paris is in 2nd place, Kyoto in 3rd place, and Osaka in 4th (source)

Kyoto

• Going shopping for souvenirs in Kyoto and need to buy a cheap suitcase? Allamanda (map) has cheap ones. However, the shop is not tax-free
• I recommend staying in Kyoto and doing 1 or 2 daytrips to Osaka, instead of staying in Osaka (which is more expensive). Take the zen garden train from Kyoto to Osaka for a unique experience. It's the same price as a normal trail but offers a much more unique experience.
• I can HIGHLY recommend the premium fatty salmon sushi at Morimori (map) on floor 8 of the Kawaramachi Garden shopping center
• Kawaramachi Garden also has Yakiniku MARUTOMI (map) where you can get different cuts of wagyu for a reasonable price
• The gionmachi neighborhood (map) has exquisite old buildings and you might spot a geisha (or maiko) in the evenings.
• You have to visit Chiikawaland on the top floor of Kiddyland (map) just to observe how crazy people are about chiikawa
• Many Indian restaurants offer good Indian food and unlimited naan bread, including Earth Cafe (map). Enjoy this perk when you're starving
• Kyoto train station is so huge that I consider it a destination. Enjoy the view from the top floor observation area (free access) instead of paying to visit the Kyoto Tower. Video of other station secrets here
• Don't go out of your way for this place, but Spice Curry Izon has very instagrammable and tasty curry dishes (map)

Kyoto Area Zen Gardens

• My favorite moss garden in Japan is Gioji (map), better than the overpriced and hard-to-enter Saihoji (map)
• Hoshun-in Bonsai Garden (map)
• Obai-ji garden (map)
• Murin-an garden, they have a cafe where you can reserve a table in advance to enjoy tea looking out on the garden (map)
• Tenjuan garden (map)
• Eikando temple (map)
• If you visit Tofukuji (map), be SURE to also visit the nearby serene Sesshu-ji garden (map)
• Kinkaku-ji (map) is a famous golden temple, very instagrammable but also busy. Not the most convenient to get to.
• Arashiyama Bamboo Forest (map) is sometimes crowded, but it's free to walk through and admire bamboo so stop by if you're nearby
• If you want to feel special, try to book a visit to one of the imperial gardens. You must reserve in advance and tickets are limited. You go on a guided tour in Japanese but they give you an automated English audio guide.

Kyoto Area Tea

• Ippodo Tea flagship store is just exquisite, get their most premium matcha and enjoy (map)
• Toraya Karyo is also exquisite, though imo it's better for the desserts and ambiance than the quality of their tea (map)
• Mandaracha offers unique cold brew tea infused with nitrogen (map)
• Chazuna (map) is a tea museum in Uji where you can book tea experiences, like grinding your own matcha or a tea tasting session. The museum also has an exhibit area so you can learn more about Uji tea.
• Tsuen in Uji (map) is a 25th generation tea shop, the oldest tea shop in the world, and one of the oldest businesses in the world
• Mitsuboshien Kanbayashi Sannyu (map) is a historic premium matcha shop that served tea to the emperor for generations. They have a small museum upstairs. Their matcha is more expensive because the brand name is associated with the emperor.
• Kyoto National Museum (map) is nice with old artwork

Kyoto Area Tea Shopping

• Ippodo premium gyokuro and premium sencha: don't look at prices, just buy the absolute best that Ippodo has. If you are at the Kyoto store, the top tier tea actually ISN'T ON THE MENU - they have a secret premium tier for the more discerning tea connoisseurs
• Matcha from Kanbayashi in Uji: This is the 16th century store that has the emperor grade matcha. Go upstairs in the store to see their museum display showing all their newspaper clippings and other history of delivering tea to the emperor. Ideally the Belgian son-in-law is working when you're there (40 year old white guy), he's fluent in English (and Japanese, naturally) and can help with any questions
• Genmaicha: green tea with rice. One of the cheapest green teas, but I like the taste and it's good for casual daily enjoyment without breaking the bank
• If you're in Kyoto, I can recommend buying tea from Mandaracha and Garden Lab. They have unique hipster offerings, like single origin teas and rare tea breeds
• Consider visiting antique stores if you want to buy an old school natsume (lacquerware storage container for matcha). I didn't buy one but they are cool. You can also find unique teapots or teacups in these stores. This is the one I went to in Uji and bought that super fancy teacup
• Gyokuro hohin: different than a Chinese gaiwan, but similar, and mostly for gyokuro
• Kyusu teapot: these are special for Japanese sencha. You could buy the one that Ippodo sells with their branding, but if you want to save some cash, you can search for ceramic stores or tea stores and buy a cheaper one there
• Ippodo matcha sieve: good for breaking up the matcha particles, useful for the most premium of matcha experiences
• Matcha bowl(s): Buy this in Uji, the capital of matcha, if you want a bowl with a cool story behind it. Basically just pick ones with a design or color you like. Also consider whether you want a tall bowl that is easier to whisk without droplets flying over the rim of the bowl

Osaka

• Visiting the Glico Running Man sign (map) in Osaka is as important as visiting the Statue of Liberty in NYC. Plus, Dotonburi is the Times Square of Osaka, very lively and packed with tourists. Go check it out.
• Amerikamura (map) is a small neighborhood where a unique Japanese interpretation of western and American culture can be seen. Very interesting to walk around.
• Den Den Town (map) is similar to Akihabara in Tokyo, filled with electronics shops, otaku shops, and maid cafes
• Osaka Castle is a must-visit if you are not visiting any other old castles in Japan. If you are visiting others, then Osaka Castle is not mandatory, because it's more crowded with tourists than castles in smaller cities like Himeji
• Umeda sky building is futuristic looking and has a nice observation deck (map)
• I did not visit, but Osaka aquarium should be amazing. One of the few aquariums that has a whale shark.

Misc. Advice

• Tokyo and Osaka are more expensive for lodging and food than Kyoto. From the cultural perspective, Kyoto is more traditional and unique, while Tokyo feels closer to a big city anywhere. I highly suggest spending at most 1 week in Tokyo and spending most of your time in Kyoto. I would aim for spending 60% or more of your time in Kyoto. A possible itinerary is to fly in to Osaka, take the 1 hour train to Kyoto and stay there for days, later take the JR West train pass down to Fukuoka, fly to Tokyo to spend a few days, and leave
• Don't be a tourist who carries their suitcase on the train from the airport to your hotel. Either take a large bus that stores the suitcases underneath or use Takkyubin, an amazing luggage delivery system that can get your suitcase from anywhere to anywhere quickly and cheaply. It's also great if you want to take the train for 1-2 weeks but NOT carry your suitcase with you during that time.
• If you are buying gifts, learn how to get tax-free shopping as a tourist. Many guides exist online, such as this one
• The most common type of rail pass that tourists get is the full country Japan rail pass, but if you do not plan to travel around the entire country, you can get better deals buying a train pass for just JR East or JR West. JR West alone has 12 different rail passes at different prices covering different parts of the country, so you only need to pay for the areas you plan to visit.
• Chain stores you have to visit just to admire them include: Yodobashi Camera (amazon.com but irl, 7+ huuuge floors), Don Quijote (great for souvenirs), 7-Eleven, Daiso, CoCo Ichibanya (curry), Yoshinoya (gyudon), Matsuya (gyudon), Sukiya (gyudon), Montbell (if you love fancy technical clothing), Tokyu Hands (rebranded now to just "Hands", great for stationary and other unique gifts)
• You can take a nice multi-day trip on the shinkansen from Osaka to Fukuoka (and perhaps afterwards take a ferry to South Korea?!?) by stopping in Himeji, Okayama, Fukuyama, and Hiroshima. The shinkansen is fast (duh) and all of these cities have castles or other scenic tourist spots. I can recommend saving 45 minutes in Himeji for the gardens next to the castle. Ritsurin Garden is worth a detour from this main shinkansen route if you like Japanese gardens (map).
• If you are dedicated to seeing the BEST Japanese gardens, travel far to visit Adachi Museum of Art (map)
• Okinawa is probably not worth a visit unless you want to stay in a resort. I found the US military presence (25% of the islands are still occupied) kind of depressing.
• Kamikochi in the Japanese Alps (map) is a very scenic hiking spot, best viewed in autumn when the leaves are colorful

Fun facts

• In Japan they don't use lol, they use wwww (source)
• Prepare for chiikawa everywhere. Watch 3 mins of videos before you arrive: here, here, and here. You may even feel the need to get a reservation for one of the new Chiikawa cafes
• If you visit an onsen and have a tattoo, they may not let you in. Tattoos are associated with yakuza.
• For a unique local sports event, attend a live baseball game.
• Kyoto has many free art galleries, I highly suggest dropping by some of them because the quality level is very high.
• To understand the popularity of those claw games, one must play the claw games.
• Because English is not very widely spoken outside of the main tourist areas, I can recommend learning 30-50 basic Japanese words (hello, thank you, excuse me, bill please, etc.). They really appreciate any effort you put into that
• Read up on some cultural differences before arriving, just to prepare yourself. Talk quietly in public places (especially on the train), don't wear shoes indoors, don't stare, etc.

Advice from friends (not my advice but these people know Japan!)

• Skip Osaka entirely, instead visit a small town in between Kyoto and Osaka. You will find the most beautiful parks and rivers with few people around, and people in these towns are just so happy to see a foreigner :)
• Rent a bike in Kyoto and get lost off the beaten path. You can find restaurants that are run just for the love of the game, with amazing food.
• When no English is spoken, google translate to the rescue. You can test google's text-to-speech mode before your trip.
• If you see a big line outside of a restaurant, cancel everything and stand in line to eat. It's always unbelievable.
• In BBQ restaurants, tell them "feed me, I trust you" and they go nuts! They appreciate your confidence in them, could strike up many friendships this way if you stay for a while.
• Try eating natto, it tastes weird at first but is a quickly acquired taste (note: engn33r disagrees on this point)
• Izakayas can be good for late night, especially if u like drinking. Very cheap too.
• Do not go out for breakfast. Ever :)