The number of pokémon Amiibo figures is not even an issue if we consider the Amiibo cards, much like was done with Animal Crossing series.I certainly have ideas how they can do Amiibo, though the question with Amiibo is how would they do with it making new ones? Who would they base the Amiibo on? The obvious answer would be the Pokemon, but with their being SO many Pokemon they can't make an Amiibo for all of them, even doing the most popular might be a bit much. They could maybe do some of the human characters though they generally aren't are marketable as the Pokemon (unless they maybe do a combination, having a notable Trainer with their ace Pokemon).
As for ideas what would Amiibo do: unlock special battles, insert a special Pokemon into the wild/make it easier to catch a certain Pokemon, unlock customization items. Though they do need to be careful not giving the player too much of an advantage, I would say not giving them a way to make a lot of money or gain massive amounts of experience would be something to keep in mind.
And since we are talking about pokémon, TPC already have the perfect excuse to make comemorative TCG cards that works as Amiibo cards.
This is not even some breaking news, because we already had some special e-cards that was compatible with GBA e-reader. Those give access to exclusive berries, rare pokémon, alternative battle arenas in Colosseum and new, special trainers with quite strong teams in both overworld and Battle Tower.