I think they expect Amiibos to have a demand similar to Skylanders or Disney Infinity.
The first wave of Skylanders (Spyro´s Adventure) had 32 different figures, some were easier to find than others, but people didn´t seem to care that much, what was somewhat curious, because Skylanders actually demand players to have the figures in order to explore all that the game has to offer. So I´d assume that people would naturally feel pissed off for feeling forced to buy figures that could be hard to find (specially those extra worlds bundles)
In the case of Amiibos, they simply decided to produce huge amounts of the most popular characters. It´s easy to find Mario, Peach, Kirby, Pikachu, Link amiibos, and the rare amiibos normally refer to characters from games that are not so popular, like Shulk from Xenoblades or Fire Emblem characters or Captain Falcon from F-Zero.
I believe that the real problem is lack of a comprehensive marketing research to feel what would be fans expectations with the product. They launched amiibos taking Skylanders/Disney Infinity as a model - taking out the forced aquisitions - but without proper knowledge of their own consumers.
What can be done by now? Increase production and distribution. And fast.
