I have to start this post, which I think we should update as more information is gathered...

A 2-3 day trip to Nicko and surrounding national park would be nice, especially to chill out after discovering Tokyo. The idea would be to stay at a Ryuken go to an Onsen and visit the temples and the nature. 

Here are some links for general information:

And this lodge seems cosy, I'll be searching for alternatives. A Ryuken with Onsen could be nice too.

http://web.travel.rakuten.co.jp/portal/my/info_page_e.Eng?f_no=2950 

This seems so very much more interesting (me wantz) :

http://nikko-inn.jp/index.html