I was only in Tokyo for five days, but one thing really stands out to me: it's pretty cheap to eat as a tourist in Japan these days. We've had really good meals for relatively small amounts of money. A sushi dinner that included tons of toro, ikura, uni and eating until we were full ran well under $40 per person. A yakitori dinner that included drinks only cost $25 per person when in the US something similar with smaller portions was over $80 each. This food was in found in Tokyo, but in areas where less tourists and expats are found such as Naka Meguro, Nishi Shinjuku and surprisingly in Asakusa (which is high up on the list of tourist destinations, though the sushi found there was far away from the temples).
There are a few reasons why the food was so cheap.
1. The currency. Since Shinzo Abe most recently came to power promising an escape from deflation, the yen has been selling off verses the dollar. If the yen were still at 80 prices would be about 30% higher from my perspective and things would not feel quite as cheap.
2. I live in SF. San Francisco is getting more expensive every year as businesses cater to many newly affluence workers that are less price sensitive than other parts of the world. Combined with supply constraints and higher labor costs this means SF meals get expensive quite quickly. Meals also feel cheaper when we don't have to pay for service separately.
3. I'm comparing medium to high end SF restaurants to average/low end Japanese restaurants. I'm mistaking authenticity for quality and comparing apples to oranges. This is entirely possible but judging by both food quality and services the Japanese restaurants are winning.
4. Japan's high prices are found in consumer staples and real estate. By staying outside the most popular destinations we've avoided the real estate issues. Outside of the high cost areas the only surprisingly high prices we saw were in the occasional purchase of consumer non-durables. These are caused by regulations which generally prevent big box retailers from entering the market and driving down prices.
Towards the end of the trip we did find some expensive restaurants. A meal at a random Udon shop in a Ginza mall was significantly more expensive than a comparable meal in SF. We also managed to find some expensive steak at a very good little steak house, which was good enough to justify its high price. Sushi at the Tsukiji Fish market was as expensive as it was in SF and the quality was similar or worse (We were comparing it to a great experience the day before in Asakusa), but we've been told that we went to the wrong sushi place at the market. We also managed to find some bad value Japanese food in an alley famous for its yakitori. The proprietress decided that us being foreign meant that we wanted our grilled skewers drenched in teriyaki sauce, so it's hard to tell if this area would have had good food at reasonable prices if we had been able to effectively communicated.
But in general, the low prices and high quality food were found by eating local styles of food in areas away from those frequented by tourists or expats. Traveling to Tokyo and trying to eat American style food and staying in Ginza or Roppongi would probably be a way to increase costs with the main benefits being more english language menus.
With inflation picking up in Japan, now might be a good time to book a trip. Just make sure you eat in the right areas of Tokyo.