I stayed at Shunkoso in Hakone-Yumoto for 7000yen/night. They have their own onsen which was lovely and was only 15minutes by walk to the train station/stores. You can also take the buy for 100yen if you preferred. (I took the bus with my luggage but walked to the stores most of the time.)
The staff speaks some English and were very helpful. I arrived early and they allow me to drop off my luggage while I sightsee and came back suring check-in time. If you include dinner and breakfast, you have to pay extra and they serve seasonal food. It was simple but very delicious. It was a great experience for me.
Below is the Shunkoso Ryokan/Onsen info:
Shunkoso's Address:
554 Yumoto Hakone-machi
Ashigarashimo-gun
Kanagawa-ken
Tel: 250-0523
Directions: From Tokyo train station to Odawara train station by Shinkansen (Bullet Train), it is a 35 minute train ride. From Odawara train station to Hakone Yumoto train station, it is a 13 minute train or bus ride.
From Shinjuku train station in Tokyo, there is also the "Romance Train" to Hakone Yumoto train station which takes 90 minutes. Once guests arrive at Hakone Yumoto train station, a shuttle bus can take guests to Shunkoso Ryokan. This shuttle bus is operated by the Ryokan Union, and it leaves the station every 5 minutes and 35 minutes past the hour. The shuttle bus fee is 100 yen for a one way trip per person.