Driving in Japan

we (6) will be travelling our from Kyoto to Nara (2 days), Koyasan (3 days) and Hakone (3 days).

We plan to pick up the car from Kyoto and to return it at Osaka, this seems a lot cheaper than traveling by Train for 6 person (especially from Koyasan to Hakone, train charges very expensive).

Is it advisable to do so?

Is it advisable to do so?

You don't want to have a car in Kyoto due to the difficulty of finding parking lots. Not sure about Nara. As for Koyasan, it is very easily accessibly by public transportation, but access by car is also convenient.

The long-distance trip to Hakone is very long and probably rather uncomfortable, considering there are six people and luggage. I am not sure how much you would save compared to public transportation (considering you will need a relatively large car), but if it saves you money and you travel on a budget, I guess it could be an option to consider.

Here are your other options for travel between the Osaka area and the Tokyo area:
http://www.japan-guide.com/e/e4006.html

I personally would never want to drive these long distances in a crowded car.