I'm sure geography helps, but it's certainly not the driver for good train service design. Cities in Japan are definitely not laid out in thin lines, and there's not just a few routes in any given city. I was living in Nagoya back in high school, and its train lines are sprawling.

Side note, there actually isn't one shinkansen from Kagoshima to Hakodate, that route would take you on 5 different shinkansen lines: Kyushu, Sanyo, Tokaido, Tohoku, and Hokkaido. But I get your point.