I don't know what can be done about it though. Japan's economy is in trouble, and the tourist money helps and hurts at the same time. It creates tax revenue, yet inflates prices for locals. Japan's stumbling economy is a factor in itself of the tourism influx due to the weak yen.
In the next few decades I fear Japan is going to go through a difficult period of cultural erosion. It needs foreign workers and at the rate they'll be entering, they won't integrate to the level that the Japanese people want.
I'd like to think I'm one of the "15%" that the article describes - I go to great lengths to integrate despite not speaking a lot of Japanese. But deep down I know that I don't belong here, and that Japan would prefer to be a homogenous society without expats like me. And I hold no hard feelings toward them for that.