The charm of Tokyo is that you can go from ultra modern to ultra traditional in a few steps, it's both playful and traditional and all points in between. And it's pretty easy to take a train to other parts if you're looking for a different sort of experience. You can't really avoid arriving in Tokyo one way or another, but you don't have to stay there. You'll always be a little on the outside of things, that's the nature of the place. It makes it all the more lovely when you connect with people.
I always feel that the opening sequence of "Lost in Translation" captures the feel of arriving in Japan brilliantly. It's anyway a marvellous film to prepare for a visit if you haven't been.