Despite housing a population equivalent to that of China*, Tokyo is nowhere as large as you may imagine
The subway is evil and will quickly deceive you into thinking Tokyo is enormous. I used to ride through the dark, maze of subway tunnels oblivious to direction, distance and time to emerge in an exciting new part of the city like magic, much akin to stepping through Doraemon's magic door. I've always had a love of maps and a keen sense of direction but when I emerged from the subway I would have not an inkling of where I was in relation to my starting point. All I knew for certain was I was right where I wanted to be and that was fine by me.
While traveling underground with no point of reference with the sensation of moving really really fast you're easily deceived into thinking that the distance between stations is vast. While the truth is that in all cases within Tokyo at least the distance between two stations is easily walked.
To put it all in perspective, Tokyo measures a mere 25km from North to South and a slightly more generous 90km from East to West. It is bordered by the Arakawa River on the North, and the Tamagawa River on the South, both of which offer great cycling escapes, which I must remember to write about in the future. East of the city is Tokyo Bay, and to the West are scenic, relatively unpopulated mountains. The mountains are home to some spectacular cycling routes, but avoid cycling on the bay lest you sink.
Now lets try a mental exercise :
Armed with these dimensions, try to imagine an empty Tokyo sized space. Next, recall everything you know about what actually exists in Tokyo, Shinjuku, Tokyo Dome, convenience stores, manga cafe's, giant radioactive lizards, Mayor Ishihara, everything. Now, force all that imagined stuff into your imagined space, sprinkle it with roughly 12 million people, wipe off any overspill and wonder at your creation! Thats a small space with a whole lot of stuff in it, therefore its only logical that the distances between all the interesting points can't be all that great.
Its not until you get off the train and try walking or cycling around for a bit that you come to realize just how close everything is. For example you can take the train between Shibuya and Ebisu which will cost Y130, involve climbing numerous staircases, some waiting on the platform, and a few minutes of travel time, or you can walk it easily in under 15 minutes
Most residents, foreign and native alike, would never entertain the idea of walking the distance between two stations when there is a perfectly good train provided to do the job for them. As a result they have a skewed idea of the true distance between places, and are living under the misconception that Tokyo is huge.
Tokyo is smaller than you think, once you discover that for yourself you'll want to cycle everywhere.
*you may wish to check my numbers on that.