Japan Trip Planning

Whytravel is going on the "road" again soon, this time to Japan.  So far, our plan is to stay mostly in Tokyo and take two "side" trips-on to Kyoto for 3 nights and another to Hakone for 2 nights.  This style of travel, taking a big city as a base and taking smaller trips from there is a favorite of ours.  As usual, we've bought a pile of books and spent hours reading online.  But we are still looking for advice, especially about how to really learn our way around and discover Tokyo.