Thanks for sharing your experience.
It's too bad you did not find Hakone to be a worthwhile experience. While Hyatt Regency Hakone is a nice hotel, that's not where I'd go to experience onsen. In fact, they don't even have rotenburo there (unless things have changed from a few years ago) and their indoor bath is nothing special. For not much more than the rate of a regular room at the Hyatt Hakone, you could've stayed in a tatami room with en-suite private onsen and kaiseki dinner / breakfast included at a nice lodge elsewhere. Plus as jpatokal said, pretty much most ryokan rooms have at least private toilets. Those rides in Hakone would not have been too expensive if you had gotten Odakyu's Hakone Free Pass.