Tl;dr – We ate a ton of food in Tokyo and Kyoto. A few restaurants stand out from the rest, which we would absolutely visit again if we return to Japan. Others were good, but nothing that we would go out of our way to visit again.
Restaurants where the food, atmosphere and service were outstanding (despite our limited Japanese language skills):
Sushisho Masa ($220/pp) – Omakase sushi. Reservation required. Every bite was delicious. Chef Masa is amazingly skilled at making each fish taste its best. It was awesome to enjoy such high-end food in such a casual and welcoming environment. Everyone in this 7-seat sushi was having a great time, including the jovial chef. You won’t know the price until you’re presented with the check, and we were shocked to see it was only $440 for two (including several rounds of beer). We must have had 25+ pieces, maybe 30, and left feeling stuffed. The two hours we spent there flew by. We would have happily paid much more for this meal.
Fuku ($30/pp) – Neighborhood yakitori joint. Reservation would be helpful but not necessary. Ordered a la carte off the English menu. The food was solid and the atmosphere relaxed. Our favorites were the bacon-wrapped asparagus and the chicken with spring onion. But everything off their charcoal grill tasted awesome.
Isetan department store food basement in Shinjuku ($15/pp) – Feast for the eyes. Bought various items (sushi, salad, dim sum, tempura) and took our food to the roof top garden for a casual lunch. Of the department store food basements that we visited, this one was the most beautiful.
Sushisei (Daimaru) ($25-35/pp) – sushi. No reservation required. It is located in an alley along Daimaru’s east exit, down a small stairway (basement level). I have eaten there 5 times (always for lunch), and every meal has been great. Sit at the bar, order beer and sushi a la carte, and enjoy the company. The sushi chefs and other patrons have always been friendly and will start up conversations. The bill never seems to add up (always seems too low), but just one more reason to love this place.
Wabiya Korekidou ($40/pp) – yakitori. Reservation suggested (only 8 or so bar seats + one table). This place blew us away. The $32 set menu (appetizers, yakitori, noodles and dessert) was amazing. We tried things that we never would have ordered otherwise and loved it all. Once the chefs and patrons saw that we were willing to try anything, the fun really started. Lots of conversation and joking (in English, Japanese, and via google translate and images), and two older Japanese women bought us a course of the most amazing pate. Highlights were the green salad, chicken tail skewer, chicken wing and shoulder, and the chicken noodle soup. This was the best chicken we have ever had. If we had found this place our first night in Kyoto, we would have eaten there every night without hesitation.
Visited lots of other places in Tokyo and Kyoto, but nothing to write home about or travel out of your way to visit: Katsukura in Takashiyama department store at Shinjuku station (tonkatsu); good ramen at Ramen Street in Tokyo Station (not sure which place we ended up at); 246 Common in Omotesando (street food park); EAT in Omotesando (burger).
Just ok: Midori Zushi (Mark City building - Shibuya) – just ok sushi that cost $25/pp (no drinks ordered). It didn’t seem much better than what we can get in the US or in the department store basements in Tokyo. But relatively inexpensive, I suppose.