Visit of Parents to Japan during Golden week

Hello all,
My parents are coming to Japan during the Golden week (April 28 - May 6). They are interested in seeing Japans culture and customs and some of the scenic places. Could someone please advise me :
1. What all places to see?
2. Since I will be travelling with my parents, should they take the JR pass ( I am not eligible as I work in Japan).
3. They are also intersted in seeing Ninja lifestyle, Japanese traditional village lifestyle and any other things.

Thank you in advance.

1. This depends quite a bit where they will stay, as 1 week (especially during the Golden week) does not allow too much travelling. I see in your profile Ibaraki prefecture, do you want to take them to Tokyo for the whole week or are you planning to show them Mito as well?

2. This depends on your itinerary...if you plan to visit Kyoto and do some daytrips to Nikko, Hakkone, Kamakura, Takayama, etc.: Yes, this will most likely pay off. If you plan on mainly going to Tokyo and explore the city by metro: this will not pay off.

3. Ninja lifestyle? As you know, there are not too many Ninjas living in Japan anymore...

Thank you Diggy san.

1. Yes I live in Kandatsu (near Tsuchiura). My plan is as follows
1 day - tokyo, yokohoma
3 days - kyoto/Osaka
1 day - Nikko or Asa Kusa and Kamakura

2. Even I am not aware of the places to see in Japan. So basically am searching for the same. Any more sugesstions ?