To be honest, I'm kinda glad they were so conservative with their first shipments, the scarcity made it a true wanted item, got a lot of interest from both casual and dedicated gamers, and even the public media, and showed to both Nintendo and Retailers that there is real interest in the Nintendo Brand and its products.
Stuff like the Dual-Cannon Samus selling for the price of a car, people importing them from other markets, and the holiday frenzy made them truly valuable in a lot of people minds.
Nintendo has proven Amiibos are something the masses want, now all they need to do is make a way to make the rare ones available for the true collectors, using Club Nintendo or the Online Store to do so sounds like the best choice for official "discontinued" amiibos.