5 hrs to spare between tokyo/ kyoto

We're heading to kyoto from tokyo for 3 days. Before check-in late afternoon in kyoto, thought we could visit a place on route to kyoto. Any suggestions? perhaps an onsen experience or exploring a place of interest. Thanks!

just because you check late in a hotel doesn't mean that you have to arrive at your hotel by 4 pm. I often arrive at the hotel in the morning and they and keep my luggages until check-in time. There are more things to see in Kyoto that you can possibly see in several months so why not arrive there in the late morning, drop the bags at the hotel and start your sightseeing?. you can even go to a onsen right there.

It can be Hakone. Lv Tokyo early morning by shinkansen to Odawara, make Hakone round trip, there is a 16.09 h hikari shinkansen from Odawara direct to Kyoto arr 18.15 h. ( But check with your luggage, you cannot have with you on Hakone round trip, either locker at Odawara station or sending one day earlier to Kyoto accommodation from Tokyo accommodation )