Tokyo to Mt. Fuji to Kyoto

Night bus is available between Fuji 5 lakes and Kyoto, and between Kyoto and Tokyo.

If you mean going up to the 5th station on Mt. Fuji (as far as you can go on public transport), then you frankly not see much or find a lot of enjoyment. Frequently also the mountain is covered in clouds or fog. If you want to see Mt. Fuji, it's actually better from a bit of a distance than being on it. I'd say a trip to Hakone would be good - you can see some great scenery of the mountain, and if the weather is bad, there are still many other things to see and do. Look info a Hakone Free Pass also:

http://www.japan-guide.com/e/e5200.html

http://www.japan-guide.com/e/e2358_008.html

Trying to see Kyoto as a day trip would be very ill-advised - the transport even by bullet train round trip would just eat up too much time. If 2 days is all you can spare, then I'd suggest you do 1½ days for Kyoto and a ½ day for Nara. Taking a bus between Tokyo and Kyoto would be an enormous waste of time. Since a full JR Pass would not be economical, you could look into a restricted discount bullet train ticket between Tokyo and Kyoto:

http://www.japanican.com.hk/en/tour/detail/VJOPENTK1/

Or else you could try ANA's experience Japan fare:

Since your time is limited in Kyoto, the 3 major must-see places are the Kinkakuji (Golden Pavilion), Kiyomizudera, and the Fushimi Inari Shrine. Your kids would love climbing up the thousands of torii gates at Fushimi:

https://www.youtube.com/watch?v=EandKTAwfOM

Toraneko - thank you for the advice.

During the cherry blossom in April, where is the best viewing area around Mt. Fuji.

Also, I saw a post about taking the slow train at various stops from Tokyo to Kyoto. Do you have any information? I cannot locate the website anymore. Thank you.

This site has info on blossoms for around Hakone:

http://www.japan-guide.com/blog/sakura13/130410_hakone.html

For the Fuji 5 lakes area etc, try:

http://www.japan-guide.com/blog/sakura14/140423_fujigoko.html

I'm sorry I am not sure what slow train or website you are referring to. There are countless places in between though.

Thank you again Toraneko. You mentioned the JR pass. Will it be worth the price if we used it back and forth Narita and Sagami Ono area, in and around Tokyo for 2 days and the round trip to Kyoto?