I don't understand why this is "considering supporting." Once Nintendo decided to go and make toys, they should have decided to implement support in most or all of their games.
I don't care how little or how big it is. The people that bought Amiibo should get some sort of support. If Nintendo isn't committed to do that, then Nintendo should not have entered into this style of game support.
So what would I like to see?
Well, for Star Fox they could make a random level generator. This would be a a quick on-rails level that takes enemies and patterns and put them together. This feature could be used to create special bonus levels designed by the creators of various franchises. (So they would use it more as a level editor.)
For Link, having themed costumes would be cool. Another idea would be just adding "Zelda" themed Nintendo characters into the world. So I can scan Princess Peach and she would appear in the game somewhere. And I can do a mini-quest for her. Maybe pick apples for her, or find a special pink apple and get a reward. Captain Falcon can race me on his "horse" and what not.