Though I'm confused has Nintendo gone to a system FC and not a per game FC? I know the 3DS has more online features and what not but I'm curious as to what a system FC does.
Yes, the 3DS only has the one friend code.
Excerpt from the 3DS entry on Wikipedia; I bolded a couple statements to hopefully answer your questions:
The background connectivity allows users to exchange software content regardless of what software is currently in the console. Sharing content is stored in a "data slot" in the console. Using this data slot, Nintendo 3DS users can readily share and exchange content for multiple games at the same time, whenever they are connected, even when playing unrelated games. Using the console's background connectivity, a Nintendo 3DS in StreetPass Mode can automatically discover other 3DS units within range, establish a connection, and exchange content for mutually played games, all transparently and without requiring any user input, even when the console is dormant. For example, in Super Street Fighter IV: 3D Edition, if the user passes someone with the same software, he has a battle to collect trophies from the other player.
It can be customized to fit the user's preferences, including opting out of it altogether for selected software. One application being considered is functionality to "automatically acquire magazine and newspaper articles", similar to networked e-book reader applications. Other improvements to online functionality include how Friend Codes are implemented, with only one code necessary for each console, as opposed to the DS and Wii where individual Friend Codes are required for each piece of software.