What can be nice is to use the Hakone Free Pass, that give 2 or 3 day of free transport.
Then you can go to Hakone-machi, Go to the srine close from there, there is also a garden from where you can see mount fuji by a clear day, then take the boat to cross the lake. From there, use the ropeway to the other side of the mountain and stop by owakudani. Then you can sleep there, enjoy the onsen. Then what I did is to go to Fujiyoshida for my third day before going back to Tokyo.