The things I look for in Hotel are mainly location, price, and facilities. When I travel with my family I prefer to use Airbnb instead of hotels. However, if I travel only with my son, a hotel is a more practical option. These are some of the hotels I have been tried in Japan.
Hotel Mystays Sapporo Aspen

Room type: twin room non-smoking
Price per night: Rp 917.000
Location:060-0808 Hokkaido, Sapporo, Kita-ku Kita 8-jo Nishi 4-5, Japan
Number of guests: 5 (4 adults and 1 child), using 2 twin rooms.
What I like:
The location is very close, just 200 meters from Sapporo Station and department store. There is a convinient store nearby. The staff is very friendly and able to speak English well. You can also store your luggage there if you arrive there before the check-in time and also after check out time. making it convenient for us to travel around without carrying our luggage.
What I do not like:
The room is pretty small for two adult and one child.
Hotel Mystays Otemae Osaka
Room type: standard apartment non-smoking room
Price per night: Rp 2,262,000
Location: 540-0025 Osaka Prefecture, Osaka, Chuo-ku Tokui-Cho 1-3-2, Japan
Number of guests: 2 (adult and child)
What I like:
I love the room size of this hotel. It is 40m2, which is quite large for 2 people. There is a big fridge, a dining table, a couch, a microwave, a kitchen, and an electric kettle. The hotel apartment also very clean, and near the train station. They also have a laundry room near the lobby which you can use by putting in some coins. You can also buy the laundry soap from the lobby or exchange your yen with coins.
What I do not like:
The hotel only fit one adult, if you are having two people it is either you both sleep in a single bed (which is very uncomfortable) or one of you will have to sleep on the couch.
Hotel Unizo Osaka Shinsaibashi, Osaka.

Room type: single room
Price per night: Rp 1,731,781
Location: 542-0086 Osaka Prefecture, Osaka, Chuo-ku Nishishinsaibashi 1-10-10, Japan
Number of guests: 2 (adult and child)
What I like:
This hotel is located near Shinsaibashi station within 4 minutes walk. The hotel surrounds by lots of food places, and very easy to find a taxi. Close to Dotonbori, and shopping places. The room size is 14 m2. The breakfast is also delicious and a child under 6 years old is free of charge for breakfast. They provide you with comfy sleepwear. There is a convenient store right next to the hotel, which is very helpful for travelers. Everything in the hotel room is clean, minimalist, modern and look brand new.
What I do not like:
The hotel is very popular; it is sometimes not available to book.
The hotel staffs are friendly but some of them do not speak English very well.
Hotel Citadines Central Shinjuku, Tokyo.
Room type: twin room
Price: Rp 3,000,000
Location: 160-0021 Tokyo Prefecture, Shinjuku-ku, Kabuki-Cho 1-2-9, Japan
Number of guests: 5 (4 adults and 1 child)
What I like:
The Location is absolutely golden. It is located in the center of Shinjuku. You can reach mega don Quijote, comic book store and Muji within 5 minutes walking distance. Easy to find and close to the train station. If you love shopping, you will love this hotel. If you walk further, within 10 minutes you will find lots of department stores around.
Heaps option for food, coffee shop and dessert places.
The staffs are friendly and speak English very well.
The breakfast is delicious
What I do not like:
The hotel is a bit expensive, but I think it is worth the price.
Hotel Monterey Hanzomon, Tokyo

Room type: Economy single room
Price: Rp 1,421,720
Location: 102-0082 Tokyo Prefecture, Chiyoda-ku Ichiban-cho 23-1 , Japan
Number of guests: 2 (1 adult and 1 child)
What I like:
This hotel location is not in the middle of shopping places or tourist places within walking distant. It does not mean this hotel is bad. I like this hotel. The hotel is located in a relatively quiet neighborhood, which is kind of nice too. It is like a refreshing change from the busy Shinjuku. This hotel is close to the train station and a convenient store within 5 minutes walking distance. If you want to go to Shibuya, it is only 4 stops away.
Another thing is, this hotel provides you with a mobile phone that you can take outside the hotel.
What I do not like:
The room is a bit old and there is only a limited option for food around the hotel. But there is doutor coffee close to the hotel if you want to have breakfast.
I like these hotels, I personally would stay there again if I am not renting Airbnb properties. The price and the room size are similar, the main point is definitely the location.
Disclaimer: the price I show you in this post is based on my own experience and also the season when I was staying in these hotels (whether it is in high season or low season), so the price might be different according to the booking date and the duration of your stay.