In a recent interview with MTV News, US Nintendo president, Reggie Fils-Aime spoke about the Nintendo 3DS and why some decisions were made with the system. Most notably, one of the questions cropped up was about Nintendo's unfavourable Friend Code system, which now been improved on the 3DS. Instead of having to enter Friend Codes for each piece of software, 3DS users now have one code for the system only.
MTV News quizzed Reggie Fils-Aime on why they are needed at all and why the parental controls couldn't just be used to help protect children from adding random people to their friend list. Reggie then responded with the following answer:
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.
To sum it up, Friend Codes are used to provide an extra layer of protection between you and an online stranger and limiting their access.
You can also catch the segment of the interview below, in video form.