Just come back from a month in Japan - BUT my husband is Japanese so we were able to get a spousal visa, and my teens have Japanese passports. Some things to think about - Japan is taking Covid very seriously. Everyone wears a mask at all times, even on an empty road. All venues are taking temperatures as you go in, and many events are still cancelled. As others have said there are no tourist visas at present, unless you go through an approved tour guide company which is v expensive.
Because of Covid even domestic tourism is being discouraged in some places and bed capacity in hospitals is being taken v seriously. Some of the places mentioned, such as Okinawa, have asked for tourists not to come.
The flights are expensive too at the moment - because of Ukraine we flew back over Alaska and towards the north pole. (Got to see the northern lights which was fantastic). This means a 15 hour flight instead of 11.
You don't say which seasons you are thinking of but the summer (now) is unbearably hot. We had to go in July for family reasons, but for the last few days we didn't even bother going outside as it was so hot. The humidity is very high and typical temperatures are mid thirties. You sweat within 5 mins of leaving air conditioning and some places mentioned would be unbearable in the summer. Kyoto in particular is renowned for the heat and was close to 40 degrees when we left. I would avoid June-September unless you cope well with high humidity and heat (i.e. think of what it would be like sight-seeing in a sauna).
Japan is great to visit in the spring and autumn so if you have some time flexibility I would keep an eye out for what is happening with Covid and book for the right time of year. It's a wonderful country to visit, clean, safe and full of amazing sights, food and we food relatively affordable this time due to the weaker yen.