If you are looking for an alternative to Beppu, I can only highly recommend the wonderful onsen (hot spring) village Yufu City (or Yufuin in Japanese).
I have to say that during our trip through Northern Kyushu my husband and I were a bit reluctant to stay in Beppu, as we had heard that the famous hot spring village is usually quite crowded. We preferred to stay in a rather quiet place, somewhere with a more local instead of a touristy atmosphere, and that’s how we discovered Yufu City. The village is situated at the foot of Mount Yufu (which is excellent for climbing by the way) and blessed with a beautiful river and healthy hot spring water; we immediately fell in love with the charm of this small town.
We stayed at a wonderful ryokan (Japanese Inn) called Makiba-no-ie, which basically means farmhouse, located next to the river, directly in the center of the village. The main house is indeed an old farmhouse with a thatched roof and a large irori (traditional Japanese fireplace) in the entrance hall, which is used as a coffee corner and common space during the day. The hotel reception and the dining room are also located here.
The guest rooms instead are located in smaller huts or cabins spread across the ground surrounding the main house. Actually, every guest has its own cabin consisting of two rooms, en suite toilet and a wash hand basin. I think the rooms were the most spacious I have seen in Japan so far; it felt like our own little home. The design is typically Japanese, simple but very nice, with beautiful tatami flooring, a low table and a couple of low chairs. There is a TV, a fridge and everything you need to prepare a nice cup of hot Japanese green tea. Towels, yukata and a warmer jacket (in winter) are provided too, and you are free to wear it anytime, in and outside your room.
Now I could start raving about the food, but then this article might never end. Let me just say there was a fantastic variety of wonderful home-cooked food, prepared with fresh local ingredients-definitely not to miss!
As Yufuin is a hot spring village, of course the farmhouse has its own onsen, a very large open-air bath (rotenburo), surrounded by rocks and wonderful greenery; a view of Mount Yufu is included too. Actually, they are two of those pools, one for men, one for women, according to the Japanese culture. However, in case you still don't feel comfortable to share the hot spring bath with other people, there are 6 or 7 private baths in small wooden cabins, which you can reserve (free of charge) and then enjoy the hot spring water in complete privacy, alone or with your travel companion. Highly recommended as far as I am concerned.
I really loved this place. Apart from being genuinely friendly in general, the owners are extremely accommodating to foreigners. You shouldn't have any problems to communicate with them. Their website is in Japanese only; however, they use an English language booking service, which also gives some information about this place. So, are you ready for your trip to Northern Kyushu?