Manufacturing, retailers, and supply chains don't work that way. You get manufacturing capacity by leasing out or building a factory. You get raw materials by purchasing contracts to supply your factory with those materials. Workers need to be hired in order to staff the factory. Custom machinery needs to be constructed and installed. All of which needs to be decided up to half a year, or longer, ahead of time. You don't "get your preorders, add a couple extra for walkins, and then build that many" - you do a bunch of complicated market research to determine what products will sell, then you buy your factory space and materials accordingly. This is how it works for games, too - except in that case you're planning 18-24 months of underpaid developers and artists instead of 6 months of plastic and factory equipment.

What you're describing is how Kickstarter works, which is so ridiculously far away from at-scale product development it's ridiculous. You know how Pebble has a kickstarter for their new smartwatch lineup? Yeah, it's not because they need the money - it's because they want the headlines of "LARGEST KICKSTARTER EVER". The product itself is already designed and in production. Doing it the Kickstarter way of collecting orders and then making the product means much longer lead times, which means more capital invested over a longer period of time, which means more risk of missing your chance to achieve maximum market saturation at the most profitable time.

The only way the amiibo supply situation will ever be fixed is if Nintendo risks large amounts of money on factory expansions and outbidding Disney and Activision. This is money Nintendo does not believe is worth risking, so we're stuck with the current situation of a toy lineup where half the characters get one underproduced shipment.