Considering the average person doesn't care about plastic Nintendo figures, it's not hard to see why retailers also don't care. At the end of the day, even if said non-toy-specialty (i.e. non-TRU) retailers had an appropriate stock, they'd still probably sell out within a few days just because of how limited shelf space they have, and for retailers, the profit is negligible in the grand scheme (especially factoring in how much customer support they have to deal with for these things, which are only $13 MSRP). If anyone is to blame, it's NoA for not having enough confidence in their sales projection.
And then there's the whole scarcity argument. A lot of people won't admit it, but a huge factor in the amiibo craze is the shortage and the possibility of discontinuation. If stock was plentiful, scalpers aren't going to hoard them, and people would feel less inclined to buy them (due to a perceived drop in rarity) which means stores could possibly be overstocked for an indefinite amount of time (just look at all the Diddy Kongs), which is very bad for the store.