1. It's really safe. You can leave your (locked) bikes on the street at night and sleep in a tent in a park and your gear won't get stolen and you won't get harassed. There's a lot of traffic but the drivers are polite and generally drive at a much lower speed than they would on a similar road in Europe.
2. It's not as expensive as you'd think. Accommodation is not cheap, especially in the cities, and you pay a lot for fresh fruit and vegetables, but if you bring a tent, eat supermarket sushi and/or cook your own meals you can get by with the same kind of money you'd spend cycling in Europe.
3. The people are very friendly. They'll help you out in every imaginable way when you get in trouble and politely ignore you when you're getting our of your tent in the morning.
4. The views are amazing. Forget the images of crowded, noisy cities you've seen, Japan is actually filled with beautiful mountains covered in lush forests, pristine beaches and quiet temples.
5. There are plenty of toilets. A small but important point for cyclists: there are tons of clean and accessible toilets on the roads and in the cities, often clearly marked on the city map that you'll get from the tourist information usually located at the central train station. Some older toilets are of the squatting kind, but usually there's also regular toilet seat available, at least in the disabled toilet.
6. There are plenty of convenience stores. These small wonders are everywhere on the roadside (the longest distance we've cycled without seeing one was about 50 kilometers, but that was very unusual). They're open 24 hours a day, have toilets and sell drinks, food and pretty much everything you might need on the road. Seven-Eleven has ATMs that work with foreign cards and Lawson Station has free mobile wifi (if you can get someone Japanese to set it up for you on a computer that's already connected to the internet).
7. You can avoid the rainy season. The European summer holiday months aren't considered the best time to travel to Japan as the weather can get very hot and humid, but there's no rainy season in the north where the temperature also stays at a more pleasant level.
8. There are plenty of easy ferry connections. We visited all the four main islands plus six small ones along the Shimanami Kaido, and ferry connections made it very easy to get from one island to another. There are short-distance ferries connecting islands as well as long-distance ones which you can use to save you days of cycling, and the prices are very affordable. Just let them know that you have a bike when buying your ticket as there's usually a small extra fee.
9. There are plenty of places to take a bath. There are public baths and hot springs in nearly every town, and once you've learned the etiquette of getting naked and washing yourself before entering the bath they're super easy to visit despite the language barrier. Relaxing in hot water is the perfect way to finish a long cycling day! Just note that men and women have to bathe separately and that tattoos are usually not allowed.
10. You can easily survive with English (and some sign language). Nearly all road signs are in English so you don't need to have a Japanese map or to be able to read Japanese. (Having a GPS really helps, though, because the maps we've found haven't been super detailed.) Even though most people only speak a few words of English they understand a bit more, and if you really need to get yourself understood you can usually find someone who speaks more English.