Interesting idea, could see this being especially popular with first party titles. People love anything Mario, Zelda, etc. Also agree with the idea of the game checking for a save instead of having to input a code. The only problem is that people wouldn't need to own the game to get the in game reward (could rent, borrow from friend, etc) which obviously isn't really a problem for the gamer but I could see Nintendo wanting to make it so that you need to own the game. If they wanted to do that, maybe they could tie it to Club Nintendo since anyone who would be interested would probably be registering all of their games there anyway. Or they could just be nice and do it by checking for a save file.
Also agree with others that they need to do something new with Animal Crossing for me to care. I put so much time into the first game and had so much fun with it but couldn't convince myself to buy either the DS or Wii versions because they were so much of the same. It was fun once but I don't want to repeat that same experience again.