Driving in Japan

Hello,
I am planning to go to Japan, 3 weeks, for honeymoon and don't know what is the best way to visit inside Japan. Some friends told me about renting a car and do a combo between car and flight. I would like to visit Honshu, Hokaido and Kyushu (North Part).
Also, don't know if there is any site with time travelling, by car, like Via Michelin in Europe, where i can check the spending time. Also, for booking an Hotel, is there any specific site, like bookings.com?
And to arrange a guide, is it possible? Like a chauffeur / guide?
Thanks for your kindly attention,
Jose

don't know what is the best way to visit inside Japan

It entirely depends on where exactly you are going. Generally speaking, a car can be very useful in rural areas and for short and medium distances.

Public transportation is most convenient in the large cities, such as Tokyo and Osaka.

The shinkansen and flights are most convenient for long distances.

Also, don't know if there is any site with time travelling, by car

For expressways:
http://www.driveplaza.com/dp/SearchTop

Also, for booking an Hotel, is there any specific site, like bookings.com?

Bookings.com lists many hotels in Japan. Other leading English language hotel reservation websites in Japan are:
http://travel.rakuten.co.jp/en/
http://japanican.com/

From Hokkaido to Kyushu by car is a LONG WAY! pretty much like going from Spain to Belgium...AND there is so much to see!. The rental of the car plus the freeway toll fee and the gas will cost a pretty penny (you are used to drive on the left side of the road are you?). It would make more sense to stay in Japan for 2 weeks only and explore 2 -3 areas close to one another in depth at a slow pace.

Agree that it's better to concentrate on small areas than drive long distances (if you are ok driving on the left that is) We recently rented a car through Tocoo.com and toured N.Kyushu and it went very well. We were based in Yufuin which is central. Then we ferried to Hiroshima and Miyajima and trained via Kyoto to Kanazawa and toured the Alps by rented car - excellent!

Japan has one of the most efficient and fastest public transportation systems in the world- I really recommend taking advantage of it. Tolls on expressways are very expensive and combined with rental, parking and petrol fees can make driving far more expensive than taking the train.

Hiring a guide/ chauffeur as you might do in India or South-East Asia would be hugely expensive and is only an option in Japan if the expense isn't an issue for you at all- you would have to be quite wealthy to even consider it.

As said, the public transportation in Japan is very good, however, this is not true for Hokkaido, Shikoku, parts of Kyushu and if you wanna visit the Japanese Alps. For those areas it's better to rent a car or motorcycle.

I second that. We prefer smaller back roads so tolls were only of the Y700 and Y400 types, petrol use was minimal 8l/100km @Y160 litre in a 1500cc auto and parking out of cities is no problem anywhere. The difference in enjoyment is huge though and the Japanese are very courteous drivers. If you are not adaptable to left side driving that could be an issue. Look at the Tocoo.com rental rates , specially the 2 day specials (Y8800) but watch the drop-off fees for leaving car at other towns - though it was only Y3100 extra from Takayama and leaving at Matsumoto for example.

Interestingly, it was only a little more to hire the car over combined bus and train fares this way.....and no comparison to enjoyment. The Nissan rent people happily dropped us and bags at our hotel if asked.