Traveling for two weeks with three kids.

Hi,

I am traveling with my wife and three kids (5, 2, <1) and two in-laws (70+) for two weeks in June (5-19). Here is our tentative itinerary:
--Osaka (5-9) --Kyoto (9-12) --??? (Hakone, Tokyo, IDK) Any suggestions or ideas would help. --Tokyo Disney (16-19)

I'm looking for suggestions as to which pass to buy and what would work from traveling from Kyoto to Hakone. My in-laws would like to visit Hakone I was just unclear with how it works.

Also, when we fly into Osaka (Kansai) can I catch a JR train into Osaka (542-0086, Osaka, Chuo Ward, Chuo-ku Nishishinsaibashi 2-17-3)?