I'm assuming this friends codes isn't the old version where each game has a different code, but you just have one friend code for the system. If so, I don't see the big deal.
Sure its not as easy to tell someone to add 85722546820 versus skippypeanut538, but easy enough. You just put it in your sig below your Nintendo ID and people can add easy enough. Isn't that how 3DS was?
But from the sound of things you can add people by either id or friend code. So again it sounds like people are bitching about an optional thing?