12 days, 11 nights (during Golden Week)

Hello,

my wife and I are heading to New Zealand for a couple of months but given our flights had to stop en route we thought we'd take the chance to visit Japan.

So we booked our flights (arriving Tokyo 0900 24/04, departing 1900 05/05) and have just discovered that this means our final weekend coincides with Golden Week, which I suppose is something of a mistake?

If Golden Week is the time when people head to the countryside I'm guessing that it makes sense for us to do non-urban things at the start of our trip and come back to do Tokyo over the Golden Week weekend?

If it was your first visit to Japan how would you plan your visit if your 12 days/11 nights included Golden Week?

Thanks

Since you are coming in Golden week you need to start booking reservations now. It might be really busy and crowded but it still will be a very nice trip.

I would get a JR rail pass and travel down to Kyoto also. Kyoto is a do not miss place in my opinion. With the JR rail pass you have the option of the 7 or 14 day pass. I would do the 7 day pass.

Day 1. You arrive. I would make sure to stay up all day to help with jet lag. I would also explore the area around my hotel/hostel.

Day 2-4. I would explore Tokyo and surrounding areas. http://www.japan-guide.com/e/e2164.html

Day 5-10. Travel to Kyoto, Osaka, Nara, Kobe.
http://www.japan-guide.com/e/e2158.html
http://www.japan-guide.com/e/e2157.html
http://www.japan-guide.com/e/e2165.html
http://www.japan-guide.com/e/e2159.html

Day 11. Travel back up to Tokyo.
Day 12. Go home

I also recommend booking hotels and everything else RIGHT NOW! It might actually be already too late for some popular spots like Kyoto, for example.

I spent my last Golden Week in Tohoku and Hokkaido. The great thing about that is that you'll come just in time for the cherry blossoms there! As it's colder than in the rest of Japan, cherry blossoms bloom later there!

You can see my itinerary of that trip here: http://zoomingjapan.com/tag/tohoku/

If Golden Week is the time when people head to the countryside....

That sounds to be a feature of rather obon and New Year week.
A business year begins from April in most of companies and schools in Japan. I suppose some of people in urban areas may remain inside the urban zone, some may make trips to suburban / rural areas.

So we booked our flights (arriving Tokyo 0900 24/04, departing 1900 05/05)
have just discovered that this means our final weekend coincides with Golden Week

Which airport will your planes use?
Golden Week 2013 will have two sets of Saturday, Sunday and holiday(s), which are 27 - 29 April and 3 - 6 May. From the standpoint of crowdedness, it sounds better to expect much time if you visit a popular and easily-accessible tourist spot in any of these days and to avoid using interregional transport modes in the evenings of 26 April and 2 May and on 27 April and 3 May. The other 3 days (i.e. 30 April - 2 May 2013) will be weekdays. Some of company workers may take the 3 days off.

Good luck!