The problem is not Apple the problem is retailers in Japan.
There are *some* locations in Japan which take NFC - like McDonalds in Japan in big cities have NFC (you can tell by the symbol ).
For the most part Felica reigns supreme with the likes of Suica and Edy. Hence why Apple is putting a Felica chip in as it will take years before Japanese retailers adopt NFC widely - hence they are shortcutting their path to market by putting in a Felica chip.