Reggie explains why they continue to use this community-hated feature.
In a recent interview with Nintendo of America’s COO, Reggie Fils-Aime, interviewed with MTV on the use of friend codes. This is what Reggie had to say about it.
“The thing that we’ve learned is that there are some games that you want to battle head to head, but you don’t want to necessarily want that other player to have full access to the space. Probably the best example is something like Animal Crossing. We may want to trade items in Animal Crossing, but do I really want the potential for you to come into my town and maybe disrupt it in some way? That’s what friend codes are all about. There are certain games where friend codes are important. There are other games where, because of the head to head nature of the gameplay, it really isn’t necessary.”
This doesn’t really answer the question seeing as how he beat around the bush the entire time. I really don’t like the friend code system and even more so when they have another code to add a friend for that game. I just wish they took it away, but like Reggie basically said, it’s here to stay and we just have to get used to it.

Well, with the 3DS at least, they only have one friend code for the entire system. It's a step in the right direction.
Nintendo already explained that only 1 Friend Code will be employed for all 3DS games.
So it's not like on the DS and Wii where you had to have several of them for each dang, game. So this is a good move in the right direction. It's not perfect, but considering that Nintendo is a family oriented company, the use of FC's is expected.
I agree it's very Nintendo, but I also don't see the problem with asking for something else. Never hurts to ask after all!