Nintendo Japan's website for Amiibo figures reveals a new bit of information about the figures. They'll only be able to store data from a single compatible game at a time.
The publisher has been touting Amiibos as having cross-game functionality, but that appears to be more limited than originally suspected. It isn't clear just yet how much of an impact this will have on their usefulness, though.
Right now, we only know that the toys store data from Super Smash Bros. for Wii U. Implementation in Mario Kart 8 and Hyrule Warriors seems to simply detect the presence of the figure rather than require them to save data.
In Mario Kart 8, players can unlock a Mii racing suit that apes the look of the character placed on the NFC zone of the gamepad. In Hyrule Warriors, connecting a figure unlocks weapons and items.
Amiibo figures will also be used for Yoshi's Wooly World, Captain Toad: Treasure Tracker, Mario Party 10, and Kirby and the Rainbow Curse. How exactly the toys will be used in those games isn't yet known, and it is possible that Super Smash Bros. will be the only game in the bunch that stores data.