Obviously, this is not an entertainment film, or your typical narrative film, and should not be critiqued at that level. It is most relevant to those living in Japan, or those who have an interest in what the Japanese judicial system is like. Rather, it is an almost documentary-like investigation into the intricacies of the flaws in a judicial system.
What Suo has done here is a public service worthy of the highest praise.
I lived and grew up in Japan for 13 years, and understood that it was not a good thing to get involved in the legal system, but Suo has given viewers a clear understanding of what it is like to be held, accused, and tried for this crime (and indirectly, other crimes). It is pretty much an introduction to Japanese court procedure. This is not something that you get to see on an everyday basis. As Suo is pointing out by making this film, it is something worth trying to understand.
As for the fairness of the Japanese judicial system, the film speaks for itself. I have no knowledge of the Japanese legal system, but what I witnessed when watching this film is the sharpest, cutting social commentary on the incredible and unbelievable flaws in the legal system, and ultimately, its lack of humanity.
Some people have commented that they do not know whether it is an accurate portrayal of the judicial system. It is, although it focuses only on this one case. Suo spent four years of intensive research to make sure that the film was completely accurate. (see: http://search.japantimes.co.jp/cgi-bin/nn20070202a6.html and http://search.japantimes.co.jp/cgi-bin/ff20070105a1.html)
If you are planning on living in Japan, have lived in Japan, or are living there right now, watch this movie. I am not aware of how the legal system has changed since this movie was made, but you need to understand the flaws of the system which you are a potential victim of, just as the protagonist of this film was. He is just one representation of the many people who have been charged and tried just as he was.