I did see an interesting theory as to why certain Amiibos are exclusive to particular stores.
Pokemon has a history in toy merchandising, so one of the biggest toy stores, Toys R Us, gets Lucario, a Pokemon.
Best Buy is known for selling cool and sleek goods, and Meta Knight is cool and sleek, so he fits like a glove.
Shulk is only really known by dedicated gamers, so he goes to the biggest dedicated gaming store, GameStop.
Target is geared towards women in terms of the products it sells, so they get Nintendo's most respectable female character, Rosalina.