Again, I am in no way try to defend their system, just trying to give another viewpoint..
I don't know how well you guys know Japan, but I can promise you that with an attitude like this, asking why all the time and suggesting options which you think are better, you will not have an easy time integrating or working there. It is a general consideration, and it applies to life there, not work environment only.
Luke Skytoddler mentioning Vietnam, Korea, China in the same sentence as Japan, and talking about RELATIVELY (to what??! Europe? US?) higher level of civilisation also tells me you need to do a lot of research on the culture/country before seriously considering working/living in Japan.
I am sure it'll get better and quicker, but don't expect that to happen anytime soon..