I disagree that Hakone is any more expensive than other places in terms of hotel prices. We go to onsens all over Kanto/Shinshu/Joetsu region and I find that places like Isawa Onsen and Yuzawa are no cheaper when comparing apples to apples in terms of hotel tier/amenities. It's just that Hakone has more high-end hotels/ryokans than a lot of other onsen areas. But there are also plenty of places in Hakone that are reasonably priced. Some of the best onsen ryokans in Japan are in off-the-beaten-path places (ex: www.keiunkan.co.jp), but they're also very expensive.

In Gora, I'd also suggest looking up Gora Hanaougi... very nice place, but not cheap (although should be cheaper than Gora Kadan). I've never stayed at Gora Kadan even though I see Gora Kadan get brought up again and again on FT.