I would strongly recommend the Hakone Botanical Garden of Wetlands (also called Hakone Shisseikaen) to people who are in Hakone area and like/love plants. The gardens itself is not that big I think that 1.5h is enough to walk slowly through the whole place. The landscaping which fused very naturally to the surroundings and the plant collections is just breathtaking. In addition to Japanese, sings are also written in English (+ plants will also have Latin names). We were there at the end of March and despite only few plants blooming I found this place just amazing.
The entrance fee was 700 yen/adults (as of March 2015), but with a Hakone free pass you will get a discount of 100yen.
The Hakone Tozan bus S line will bring you in front of the gardens's entrance. You can take the S line from Gora -koen (Gora Park station) which takes about 30min to reach the botanic garden.