I was very lucky to have the opportunity to visit Japan, one of my favorite countries for travel.
I am not good at writing travelogues, and therefore I will write in bullet points about certain significant aspects of my trip.
Travel planning and season
First and foremost, if you are considering traveling to Japan, go to japan-guide.com. This is the ultimate website to use. It's super helpful and even includes sample itineraries.
Japan offers four distinct seasons. The best are Spring and Fall, respectively, for cherry blossoms and foliage. This is also the time when crowds and lines exist. But don't be intimidated, because domestic tourists are polite and disciplined. People always line up neatly, even to take photos at vista points. Winter is also ok for skiing and the famous snow festivals in Hokkaido. In fact, some of the world's best ski resorts are in Japan. Summer is to be avoided, because it's very hot and humid, unless you are visiting the Okinawa islands in the south for their world-class beaches with turquoise water and white sand. Do note, however, that typhoons hit those islands from time to time in the summer and early fall months. Make sure your air tickets and hotels offer refunds.
Transportation
There is not much for me to add: Japan's public transit is excellent and second to none. Their trains are more punctual than their Swiss counterparts. However, note several things:
In major cities, there are often the subway, commuter trains, and long-distance trains. Not all trains are operated by the same company and your JR Rail Pass only covers trains operated by JR (which used to be owned by the government) and perhaps local transit. Some rail lines are operated by private companies, and these lines are not covered by the rail pass.
In Tokyo, some subway/train stations are massive. Be sure to use Google Maps to figure out the best exit to use to minimize walking to your ultimate destination.
Beside the well-known JR Rail Pass, there are air passes offered by Japan Airlines and All Nippon Airlines. These are discounted airlines for non-Japanese visitors. One big benefit of these air tickets is that you are allowed two pieces of check-in bags--if you don't purchase this special ticket, then you will have to pay for check-in bags separately.
https://www.japan-guide.com/e/e2364.html
- There are some parts of Japan that are best toured with a rental car. I hired one to traverse Northern Kyushu and stayed at remote onsen ryokans for stunning scenery and unforgettable meals.
Safety
Japan is perfectly safe. I never had to worry about pickpockets or thefts. In a crowded cafe, I left my cell phone on the table and went to the restroom for 5 min. It was still there when I returned.
Absolutely no need to bring anti-theft purses.
Language
Though most locals have limited English capability, signs are usually bilingual. The most challenging part, is to make restaurant reservations. As in Europe, eating at highly-rated restaurants requires advance reservations. I took two years of Japanese and therefore could make bookings over the phone. However, many places offer online booking too (check Google Maps).
Cash and credit cards
Japan trails the US in the adoption of credit cards and phone payments. Cash is still preferred, particularly with small vendors, though VISA and Mastercards are often accepted too. I did not bring my AMEX or Discover with me.
Not all ATMs accept foreign bank cards, but those in 7-11s do. This was where I pulled out cash. A small fee was charged, but the convenience of finding 7-11s everywhere more than made up for this charge.
Restrooms
Most restrooms are very clean. In fact, some are cleaner than hospitals in the US. Many convenience stores offer restrooms to customers. I did use the WC at one 7-11 without buying anything but wasn't given any dirty looks. At stations and in public parks, the WCs are free.