9 days tokyo/hakone/nara/osaka

been to tokyo,osaka and kawaguchiko last year. This time plan to go hakone and nara. Arrive tokyo on 17 Mar and leaving from Osaka on 26 Mar. Here are few question :
1. How should I plan my itinery? anything special at Hakone and Nara? or any other suggestion?
2. Please advise the transport to go around this few places? Is it worth to take JTB 2 days tour to Hakone for 19900 yen?
3. How to go Osaka from Hakone?
We will be travelling with 2 younger children age 9 & 4, is it too much for them?
thanks for your help.

How should I plan my itinery?

1) Sort out the places you want to visit
2) Work out a good order of visiting them
3) make reservations

anything special at Hakone and Nara?

Not that I could think of. But it is school holiday season. Places popular among kids and families will be more crowded than usual.

Please advise the transport to go around this few places?

I recommend a Hakone Free Pass for Hakone.

Shinkansen for the long distances. Depending on where you enter and leave Japan, a Japan Rail pass might make sense.

3. How to go Osaka from Hakone?

Here you go:
http://www.japan-guide.com/e/e5206.html?aFROM=2157_5200