Why the mistrust?
I've lived in Japan for almost three years now, and I find the treatment of most foreigners in Japan is, in my opinion, fine. However, the potential damage of chipping, tracking, and who knows what else, will, I'm sure, deter people from traveling here.
Why such mistrust of foreign nationals? There is a genuine lack of understanding of foreign nationals in Japan.
I do not want to generalize, as I have many friends that think and know differently. These people have, however, traveled abroad. The IC card is a disgraceful act of invading personal privacy, and a foreign national should have the choice to enter Japan without the barrage of red tape. Japan is outdated with its policies on foreigners entering Japan.