The Hakone day pass is worth getting because there's a standard tourist circuit of (if I remember correctly) train, bus, aerial tramway, funicular, and bus again for getting around the park.

I, too, wonder why you are going to Hokkaido in April unless there are some people you want to visit. It may be hard to find hotel accommodations in Kyoto during cherry blossom season, but not in Tokyo, and you can see cherry blossoms in Ueno Park and along the Sotobori (the canal south of the Imperial Palace that used to be a defensive moat), as well as in other places.