I will be the first to point to Debito's web site for in-depth information on human rights problems in Japan (and on a few other issues), but in response to Mike's plea, I will also add that I agree. Using Debito's site as a general picture of life in Japan is not the way to go. FWIW, his latest book is a good resource for establishing oneself here, but it also seems to have a lot of similar overtones (protect your butt, watch out for no. 1).
Life here is what you make of it, but it also depends on what you bring to the country. Example: want to work? Have the necessary qualifications or be prepared to wallow in self-pity (especially on forums like this one). I strongly suggest coming with a prepared mind, and keeping one's eyes open to the reality of a different culture (daily life and business life included), and being prepared to adapt to many (not necessarily all) of the differences. Leave your own morals in your own country, or at least keep your mouth shut before complaining about any foreign country's differences as being "wrong".
Prototype,
If you can do the above, you'll be just fine. Expect a few "No Foreigner" signs here and there, expect some stares from the local populace, expect rigid immigration officers and their "guidelines", and expect to need some Japanese language skills to survive (and enjoy) daily life. Beyond that, Japan is yours for the making.