Kyoto
Notes: Kyoto is the old capital of Japan, it has a fascinating mix of traditional and contemporary you can explore.  The commercial and entertainment areas part of Kyoto is easy to navigate as it’s set up in a grid system; Kiyomizu temple is on “ichi-jo dori” or basically first street, JR station is on Shichi-jo (kinda like 7th street, and 6 blocks away from “ichi-jo dori”).  One of the famous traditional areas of Kyoto is the Gion district.
---Temples -
-Kiyomizu temple (Kiyomizudera) – Iconic Japanese temple, lots of great view and very symbolic of Kyoto. One of the must-sees.
-Kinkaku-ji – Also very iconic of Kyoto, it’s a temple painted in gold with a rooster on top.
-Fushimi Inari Shrine – A very popular shrine for tourists and photographers, it has several hundred red Tori gates lined up creating hallways of gates to walk through with statues of foxes.
-Kitano Tenman-gu Shrine (cows everywhere, known for bringing good luck towards exam takers)
---Tourist attractions
-Nijo Castle – A sprawling beautiful large castle, not sure if you can go into the guard tower but the courtyards surrounding the moat are beautiful.  You may be able to catch traditional Japanese music performances, food stands (like festival food) as well.
-Arashiyama – The bamboo forest, very cool, haven’t been there before but people rave about it.
-Gion district – A more historical and traditional Japanese area of Kyoto, it’s unique in that you can often see geisha walking around (you’ll rarely see that in Japan in general), sometimes monks walking around, and older style buildings as well.  Also apparently there’s some fun things to do at night.
---Fun areas
-Sanjo and Shijo are fun to walk around and see the various stores and food stands. There’s also a game center (arcade) that used to be super popular for years called a-cho on Sanjo-dori.  It’s still there but not as amazing as it once was, should still have a good amount of rhythm games though.
-Kiyamachi-dori – If you’re looking to bar hop, maybe make a few new friends with some Japanese folks, I’ve popped into a few bars and made random conversation with random Japanese people.  It’s also by a river with a bunch of cherry blossom trees, so very nice to see too.
-Nara deer park – It’s pretty close by, very popular.  You can feed and pet the deer.
---Food
-Kobe is pretty close by if you want to try their beef.  Most people here’s don’t see the big deal and it’s kind of a tourist trap so be careful if you do.
-Katsukura is a popular pork cutlet shop, worth it.
-There’s a few kaisekis in Kyoto, they’re expensive but unique experience.  If you’re a big foodie, it’s worth checking out, otherwise it’s pricey and may not be filling.

Tokyo
---The airport: Haneda and Narita are not in Tokyo.  If you land in Haneda, you can take the Keikyu Kuko (Airport) line but JR pass won’t work, or the Tokyo Monorail, where I believe the JR Pass will work.  If you land in Narita, take he N’EX Train to get to Tokyo (Most other options cost about the same, N’EX is fast, comfy, and most convenient).
---Notes - The popular hubs will be areas like Shinjuku, Shibuya, Harajuku, Ginza, Roppongi, Akihabara, Ikebukuro, among others.  Many popular areas are accessible via JR.  Taxis are a viable option but avoid when possible; they get REALLY expensive.
---Sightseeing
-Asakusa has Sensoji Temple and the Lightning Gate.  It’s a gigantic lantern, you can’t miss it.
-Imperial Palace – Off the Tokyo stop on the JR Line, also a great place to stop by.  It’s where the new emperor was recently minted as well (since Japan just started the new Reiwa era).
-Ueno Zoo – Something to do, I heard it’s a nice zoo though.
-Tokyo Tower, Tokyo Skytree – Tokyo Tower used to be one of the largest broadcast towers in Tokyo, now Skytree has taken over.  Both are worth a visit to go up it.  One of them has a Kirby café pop-up….can’t remember which.
-Shinjuku red light district – Kabuki-cho is the famous “red light district” where people go to drink, have a “good time”, or just spend the night finding snack bars.  If anything, it’s worth walking through for the spectacle.  Just don’t make eye contact with anyone trying to get your attention.
-Shibuya Station – Hachi-ko exit : There’s an iconic statue of the dog Hachiko, which is famous statue in Japan.  It’s a popular meet-up spot, near the famous massive Shibya Crossing.
---Fun things
-Game centers are easy to find. Places like Shinjuku and Akihabara are just chock full of Sega and Taito game centers.
-Nissin Cup ramen museum (NOT the Shin-Yokohama Ramen Museum)– This is in Yokohama which is a bit of a trip by train but worth it.  You can make your own bagged ramen from scratch to take home (but you need to get there at opening to get tickets, super popular), or make your own cup ramen to take home as well.
-Anata No Warehouse (Your Warehouse) – HUGE entertainment center in the theme of an old Chinese city, the walled city of Kowloon.  It has an ABSURD amount of games, music, traditional, specialty, fighting, vintage and classic, UFO Catchers, pool tables, you name it.  It’s possibly one of the largest and hands-down coolest game centers/arcades I’ve ever been to.  It’s in Kawasaki which is closer to Yokohama.
-Robot Restaurant – If you go to Kabukicho, you will likely walk by this big colorful display.  It’s like Medieval Times, they have a huge cheesy show with costumes, robots, lights and performances, the food is….well, it’s not really a restaurant.  It’s pricey and take a few hours but definitely a worthwhile watch.
-Maid/butler cafes – It’s not a creepy as it sounds, but it’s a unique experience when you go with friends!  I do recommending checking one out, particular chains like Maidreamin’.
-Animal cafes – If you’re an animal guy, do research on animal cafes before you go.  Several are known to be bad towards the animals and it shows.
---Food
-Tsuta and Nakiryu are popular Michelin rated ramen shops, I’ve heard is very worth it.  Go there early in the morning to grab a ticket, so you can come back later and grab your bowl.
-Kikanbo uses a “numbing spice” to add a new dimension of flavor for their ramen. One of very places that use it, not necessarily spicy unless you want to make it that way.
-Tonkatsu Marugo, haven’t been here but was highly recommended to me.
-Utage Sushi also was recommended to me.
-If you can get lucky, famed chef Jiro and his son have their shops too in Tokyo.  But wait lines are pretty bad.

If you need more places, let me know, I can definitely pick up more places to go.