Well, the only problem with Friend Codes is that you have a cumbersome number, and you have to exchange that number with somebody else first.
So, even if Nintendo forced third parties to use FCs, there is no reason the third party can't create an online community around the Miis, then store all of a users' FCs there. I mean, you can still use the FC system, but as long as you don't show the end user some 16 or 20 digit number, and you centralize the FCs in a common database, you're right where any other online system is.
It's much ado about nothing, IMHO. Just because Nintendo has chosen a poor, unintuitive system for their games and don't offer a global browser to initiate matches, that doesn't mean other devs have to do the same thing in the exact same way, even if they are using Nintendo's network and/or code system.
