This post originated as a comment to this entry on the eminently readable blog of a scientist living in Osaka. Midway through writing it, I remembered I had my own soapbox for that sort of drivel: better than crowding some innocent bystander’s comment section.
Usual limited-interest-topic disclaimer applies: unless you are have a vested interest in getting your PhD (in Japan), you are better off skipping this entry and waiting for more pictures of awesome Shanghainese moped-riding cats.
By and large, I agree with everything Jan wrote. The operative quote, I think, is that it depends more on university/faculty [and advisor] than anything else.
As a freshly-graduated PhD student (from a Japanese university), I figured I could offer some extra pointers, gleaned from personal experience and that of close friends in similar situations at a couple “major” Japanese universities: