There was a time during the early 1990s when the yen actually went above 100 yen = US$1.
As one who works for Japanese clients and gets paid in yen, I'm happy to see the yen rise. It's been tough lately with the undervalued yen.
Even with the higher yen, Tokyo is still not outrageously expensive. One of the best things about Japan is that you can go quite far into the low-price ranges and still not have to worry about cleanliness or safety. An 8000 yen single in a business hotel will be small and Spartan, but there will be no mold in the bathrooms or drug addicts in the hallways. A 1000 yen lunch in the basement of an office building is quite affordable.