Tokyo is a huge city, and you can't ever hope to see it all no matter how many days you schedule. There are some big touristy things to see there if you don't really care about the true Tokyo experience (just wandering around some of the back streets in Ginza, spending some time at Yoyogi koen or Inokashira koen, going to obscure areas, etc) that you can do in just a couple of days. If I had to choose between Nikko and Kyoto, I'd choose Nikko. My wife and I went to both places last time we were there, and Nikko was superior. There weren't as many sites to see as in Kyoto, but it was much more rural and gave us the "authentic" Japanese experience (i.e. not old sites in a huge city, although that is just as Japanese as anything else). If you scrap Kyoto, I'd recommend spending a day at Kamakura, south of Yokohama. There are some incredible shrines and temples there that are very worthwhile.