Glad to see that Tokyo hasn't changed much.
It looks like you only just scratched the surface of the city.
You will have to go back for the rest

You did not get to Ropongi area? where was the mandarine hotel situated?
The river boat ride is superb, plus the temple gardens,fantastic place to visit, plus on a Sunday outside the Olympic swimming pool and the TV studios, the road is closed off and the street is full of bands playing live, some very good.
Did you get to try "shabba shabba"? where you have the food thinly sliced and you cook it in boiling water in front of you?
Was the cherry blossom on the trees? if so, the Japanese get litre bottles of Saki both cold and warm and sit out having picnics under the trees in the evening.
Do the train station ticket offices still have abacus's? very strange to see that was.
We took the Shinkansen to Fujiama, then on to Nagoya, then Kyoto (fantastic temple gardens) then took the local trains to Kobe and Osaka. Then back from Kyoto on the Shinkansen, to Hiroshima. This is a must visit.
I think you all will have to go back for a fortnight!!:D