Having the ability to buy the content from the E-shop without the figure would get rid of most inclination to even buy the Amiibos.
"Wonderful idea, buy a Pikachu amiibo, you can dress up as Red or Green from Pokemon Leaf Green/Fire Red in Pokemon X or Y. Or you could pay like $1-$2 for the costume, but you won't get this awesome figurine!"
Yeah, most people will go with the $1-$2 route. Having the skins exclusive to it is fine in my opinion. Its something worthwhile to a lot of people, but its not mandatory. Not to say I discourage more skins available for sale on E-shop, but exclusive amiibo skins should stay that way. Its not screwing people over horribly.