well-
This being hypothetical and all if they decide to make use of amiibo with the games- the figures could act as a way to:
interact the figuring with other games, like maybe Smash Bro, like, you train your Pokémon in the game, "transfer it into the figure, then make it playable in Smash Bros.
or-
some RPG game that allows you to have a Pokémon join your party in the quest.
maybe the figurine could be a Pokeball that you can carry it around and then trade it to another person who has a Pokeball without your 3DS.
perhaps the figurine could be interactive with the Wii-u and a future game like an XD remake or sequal.
I know I am just tossing out thoughts and ideas, or wishing- but this could be a new thing to boost the game play up a bit.
Personally- I like my idea of the Pokeball tradeing mechanic. Carry a few on you, trade. Heck, I will expand a bit on the idea.
The Pokeball figure could be a mobile wonder trade sort of thing. You walk by someone, they have a Pokeball- the trade happens and you get a random trade with out wi-fi or a 3ds.
And even though like I said this being an "if they do mix amiibo with Pokémon games" sort of discussion and the "they could make it do this......" sort of discussion- I would not be surprised if they do nnot already have some sort of plan to make a good full use on a gadget with the top game titles.
Heck, look at the Zelda games: a link figuring for a Zelda game to equip or alter weapons (since link carries so many as it is)- look at the possibilities that could be done with the technology for what it can do if they took a different approach to changing how games are played with a player being able to make personal changes in the game to make the playing different each time you play? And you did the changing to it?
This allows for the player to build into the game, limited in changing the game itself but the content with in as far as taking like a personal data disk to a friends and plug in your customized character to change up the game play to make it different, add a level, ect.. I hope you see my point.