Interesting read! I think the biggest advantage / disadvantage is the double-edged sword of there just not being a lot of startups in Tokyo. It's really easy to cut through the noise and stand out, but at the same time, there's not as much of a high-quality community of people doing interesting things.
For anyone looking to experience the Tokyo startup community first-hand, we're going there next month with Hacker Paradise (hackerparadise.org) and will be throwing a number of events with the local tech scene.