The 3DS itself has a universal friend code that is used on all the 3DS games and applications the player uses. It means they only need to add a friend once, by adding their 3DS code, they can play multiplayer in any 3DS game that supports it.
For regular DS games, it is the game itself that has its own code, so you'd register your friend's Soul Silver friend code on your own Soul Silver, etc, whether you play it in a 3DS or the older models.
You could not though add someone's Soul Silver code to the 3DS friend list.
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