I'll just say what I would have done.
The figurines they have released so far are fine, keep making those so collectors and fans eat them all up.
But to make the multi-game usage easy and understandable, I would have kept amiibo unlockables inside colour classes (similar to what Skylander does). The base of the figure indicates what class your amiibo is. The game would then unlock features depending on the colour class, it could even be colour coded in the amiibo icon on the game's boxart.
Keep the classes simple with few colour choices like for example red, green, blue and yellow. Multi-game compatibility done easy, simple colour charts can detail them, then there would be no need to buy new amiibo for extra content if you own any of the four types.
Extra personalized skins as done in Mario Kart 8 or Mario Maker could still be done, but extra content like in Splatoon could be unlocked by the Squid amiibo or other green amiibo class like Link/Luigi/Yoshi/etc.
