The advantage of Hakone is that all Kodamas stop at Odawara, which is only the fourth stop out of Tokyo, about half an hour.

Although the Kodamas stop everywhere, the Hikaris, the other kind of train you can take on a JR Pass, vary in where they stop, but they tend to stop at Shizuoka, which is another half hour down the line, so you can take a Hikari the rest of the way to Kyoto.