Super Mario 3D Land's non-game-related surprises aren't limited to the absence of a full physical manual; Japanese copies offer a new 3DS firmware upgrade, v2.2.0-4.
Initial reports indicate that the update is mandatory to play the game, and that it adds anti-piracy protections designed to block flashcarts. It’s also said to add a button in your Friends List that lets you join a buddy’s game in progress (presumably if the game has an online multiplayer mode and support for this new feature).
[Update: Other Friends List enhancements include the ability to quick scroll through your list when holding down left/right, and your friends that are currently online will now appear at the front of your queue.]
It appears that this is not the same 3DS firmware as the one planned for release later this month, which will introduce video recording, 3DS-to-3DS software transfers, StreetPass improvements, and a bevy of eShop features (demos, DLC, etc). We will update this post if we hear more news about this firmware.
See also: More Super Mario 3D Land stuff