Nintendo has made things slightly easier with the Nintendo 3DS and needing only one universal friend code that you can exchange and then use for any multiplayer games you play. There wasn't however a good messaging system.
Nintendo plans to right this wrong by releasing an app for the 3DS titled Letter Box this Thursday. According to Nintendo, users can then send messages back and forth. Though that's not all, they're also able to send each other photos, sound effects, even drawings.
One would think this could be a potential hazard in online safety since you're technically able to send a picture of "anything" as well as draw shapes that aren't exactly G rated, though I'm sure the fact that it will rely on Nintendo's friend code system will eliminate such threats.