I think regarding to NFC, it really depends on where you live. I was commuting on a JR line, and having Mobile Suica combine with Edy was such a boon that I could forget my wallet I wouldn't care. Just having your phone means you can ride the train, buy anything at the convince store, pay the restaurant (you may have less choice, but there's a lot of them accepting Edy or another service), buy music or electronics, and buy drinks from vending machines. It's almost surreal how much you can do.
I later moved to the Keikyuu line and it was still great, but less magical.
In terms of technical control, Apple already choose "standard NFC" (at least that's the quote I have on the liveblog), and I would guess they are bound by Visa and Amex for the implementation. A priori Felica is part of the NFC standard, IF it supports the encrypted protocol it should be OK to have everything as third party apps.