Almost everywhere is clean and of really good quality, even hole in the wall food stalls and cheap hostel lodging (except the cheap impersonal AirBnBs, which are just like they are anywhere, though a bit cleaner).
Don’t feel like you need to spend a lot. I think the most authentic experiences won’t even be the luxurious & expensive ones.
The most accessible+affordable for foreigners might be guest houses, catering towards English-speaking clientele in particular. They can be pretty nice, and have nice touches e.g. serious coffee or craft beer. Thanks to Mike for the heads up on LEN Kyoto. ;) For me, guesthouses are a little noisy and overly social, in that public spaces & kitchens are convenient but can lead to involuntary socialising. Also, I like sleep and appreciate the Japanese norm of being quiet for your neighbours. Excited awake-at-various-hours foreign tourists do not adhere to that norm.
My favourite accommodations are simple B&Bs with tatami mats, futons, lovely breakfasts, and great baths — in many places, real hot springs. Places where you can (optionally) chat with the proprietors, who will genuinely want to help you out with recommendations and guidance. I ask for an eastern style room, so long as you can set up and fold away the futon.
Minshukus are Japanese bed and breakfasts — fun and cheap. A family or property owner living in a largeish house will rent 1–2 bedroom to travelers and will sometimes serve in-house meals. It’s a good way to experience life in a Japanese house. If your budget is tight, then these are a good way to go (over ryokans, which can get very expensive). (They do feel a bit harder to find, with the advent of AirBnB perhaps?)
- Eat a good breakfast wherever you’re staying.
- Cheap hotels aren’t bad quality. They will be basic but clean and totally sufficient. I booked multiple last-minute inexpensive hotels off booking.com, etc., and they were comfortable, professional, courteous, and accommodating. (Nothing like a cheap US motel!)
- Stay at a bed/breakfast type guesthouse or ryokan over a hotel if you can. For a short stay, the clean simple functionality and predictability of business hotels (e.g. Toyoko Inn, Rembrandt) can be nice, but they can get really drab and tiring over time. Just, utilitarian.
- AirBnBs are on the rise in Japan. The automatic translation function makes comms a little weird, but AirBnB has a strong enough cross-cultural culture and norms that somehow it works okay. Many places can be pretty impersonal and utilitarian. Some are simple, like staying at the house of a friend (UK home stay style) who didn’t do much prep for you, like cleaning.
If you’re traveling in an area full of temples, you can also stay in them. They’re inexpensive and provide delicious vegetarian meals but they also require you to attend a morning service. An interesting option.
Alternately, for adults, you can do a night, or hour, at a quirky variously themed “love hotel” of your choice, for fun. Privacy assured. An array of choices. I haven’t really kept up with their economy, but they seem to be around, including on e.g. booking.com, where they are not labelled, but you can usually figure it out. I’d visit the place’s website before booking.
Hostel and ryokan strategy?
From limited experience (I almost always stay with family and friends) a good “hostel” in Japan can actually be more like a ryokan than like what you expect from hostels elsewhere. Also, in a traditional ryokan, there are many rules and you could easily offend without knowing what you’re doing. If it’s problematic enough an offence, mortifyingly, a staffer might have to tell you. But mostly you will remain obliviously offensive.
It could be nice (and affordable) to stay somewhere first that really welcomes and helps foreigners adapt, so then when you go to the traditional ryokan you know what you’re doing and can be appropriately polite and conscientious.
Rules, e.g. in hot springs
Generally, check on all the rules. For example, with hot springs, nakedness, the art of washing up properly before entering (most crucially!), what to do with long hair, connotation of having tattoos, possible variations on gender mix rules and related signage, what to do with your small wash towel. Especially if caucasian and/or tall or otherwise going to stand out, like if prone to turning bright red in hot water. You will just have a much nicer time if you know the basic protocol, and it won’t be intimidating to go, you will get stared at less, and everyone will be more comfortable — especially if you’re properly clean!
- If you’re strict vegetarian, things will be very difficult or you’ll have to plan your food well to eat at all decently. I can attest, and speak to this more upon request. Ask about options before you even think about sitting down. Don’t expect requests to be adhered to.
- A general rule for good food: Pick places that specialise in a particular food, like soba noodles, shabu shabu, ramen, teppanyaki, tofu, tempura, because they will have to be pretty good at that thing. Small “Japanese cuisine” restaurants with one chef can be really nice, too.
- The most delicious restaurants can be tiny ramen or curry shops on cramped streets, where you squeeze in, yell out your order to the guy behind the kitchen counter, and slurp it down happily. Or five-seat corner sushi bars where you select from the day’s menu and the chef prepares and serves each piece to you.
- If you’re a seafood person, go to pre-dawn Tsukiji fish market in Tokyo. See the huge trade. Then you eat at places around the market. I don’t know the new market, though.
- One Japanese cuisine chain that has always been consistently quite tasty (to me) is Ootoya, at most train stations in Tokyo. Fast casual and fresh. Very reliable. Tasty but healthy. Look for the sign; it’s often on an upper floor. Obey the protocol for ordering. (New Yorker even wrote it up.)
- If you meet a longtime-Tokyoite foreigner who can take you to his country’s spot, go. Tokyo has excellent Italian, Indian, Chinese (all sorts), Thai, Nepalese, Malaysian, etc. There’s even a legit Mexican spot in a hidden location down a flight of stairs in Harajuku, sometimes with a proper imported mariachi band performing.
- If you want authentic foreign cuisine, avoid country-specific restaurants that are obviously geared/adapted towards Japanese people. In smaller markets where they really need to cater to local preferences to survive, it might barely resemble the original cuisine.
- Izakayas are great places for drinking and eating. They offer small plates of food (like a tapas bar), so you can experience a wide variety of dishes. You see a lot of office workers de-stressing there after work. The chains are not bad. Good for a quick bite. Avoid if you hate smoking.
- We also like to go to standing-only salaryman bars for a nama biru (draft beer) and kushi mono (food on sticks — meat, quail eggs, veggies, etc). [This input is primarily from a friend.]
- Unless you want that specific experience — like super popular crazy cheap conveyer belt sushi places — skip ubiquitous Japanese chains, especially with English names, or else you’ll find yourself eating at the equivalent of a Denny’s, sometimes dropping a good amount of cash on an extremely mediocre pizza. There are also actual Denny’s restaurants.
- Think critically if a restaurant seems tooooo accessible to foreigners, e.g. English listed prominently or first on signs or menus. I suspect that it’s easy for places to get away with not being so authentic or good when their clientele is passing through.
- Find out the specialty food for that particular town. Every region has overarching regional foods (e.g. type of noodle), and every single town has its specialty food, and some of them are amazing. Also, the region’s specialty foods are available for takeaway, such as at your local bullet train station. Always very well wrapped. Generally meant for gifts. (Of course, all those “specialties” are all also variations on a small number of themes: rice, dango, noodles, broths, various ways to prepare a soybean.)
Sample of local specialties in my area, food and otherwise: soba noodle eating contests, goma suri dango (ground sesame seed sweets), mountain vegetable soba (sansai), curative properties of the local hot springs, mixed seeds/grains to add to rice, a mysterious road where you put the car in neutral and feel like you’re going up hill, paper-making (washi), cast-iron teapots and bells, round crackers made of wheat (not rice!) with things like peanuts and sesame seeds, the skilled local matchmaker, the baby-crying sumo competition…