The most significant attraction in Tokyo I think is the mixture of tradition and new. There are hundreds of skyscrapers but at the same time there are shrines and old buildings.
Visit Shinjuku or Shibuya to feel the metropolitan atmosphere of Tokyo. Then visit Ueno, Asakusa, or Yanesen to feel more traditions. Don't forget to visit shrines and temples. Eastern side of Tokyo has developed from long time ago so there are more traditional atmosphere left in the east side, comparing to west side.
Seeing the difference of the cities, and this mixed style is one of the experiences I think is unique in Japan.