Best way to get around Japan with our plan?

My family and I of 4 adults are planning our trip to Japan in 2014 February. We will be arriving on the 5th and departing on the 18th.

We are arriving in Osaka, then after a few days travelling to Kyoto for a night or two, then to Fuji Q Highlands themepark where we would like to stay for one night, and spend the remaining week in Tokyo.

What would the best/cheapest way for us to travel around for the 2 weeks? When we're in Tokyo we'd like to explore some of the outer city areas also, so I guess we will be catching the train very often.

Is a JR Pass the best way for this or is it cheaper to buy individual tickets?

Thank you !

A 7-day JR pass will only pay off if you visit somewhere else, e.g Hiroshima/Miyajima. Use www.hyperdia.com to calculate costs. You need to surpass 28300 yen to make it worthwhile.

An IC card would be a good purchase, as it will cover most of your transport in Osaka, Kyoto (not the buses) and Tokyo. They're not a discount card but are very convenient. http://www.japan-guide.com/e/e2359_003.html

Thanks for that! I will have a look into it.

On another note, does anyone know any hotels in Osaka, Kyoto and Tokyo that will allow 4 adults in one room? I'm having trouble finding ones that have either 2 double beds or 4 single beds, or allow more than 3 adults in a room in general.

No problem.

I did a wotif search and the only one that came up in Tokyo was Sheraton Grande Tokyo Bay Hotel. You may want to look at ryokan, hostels or apartment rentals. Try Jalan, Japanican, hostelworld, Japanese Guest Houses, airbnb or a Google search for specific places.

Sheraton Grande seems ok ! Thanks for that!

Would you say it's more worth it to get the JR pass if we used it to go to Gala Yuzawa for a ski trip or something?

Just to be clear, would it be easy to get from Osaka to kyoto, kyoto to Fuji Q Highlands theme park (Im not sure which station we get off at for this themepark... If someone could let me know that would be great too!), and then Fuji Q Highlands to Tokyo? Or is that too complicated.. We don't know much Japanese so horrible if we got lost!