Or Nintendo can do preorders way ahead of time and not set a limit. To me, this seems like the most logical approach a company could take if they are really that worried about printing too many. And it is kinda the point of pre-orders, I think, is to get a general idea of demand.
I just simply will never understand the point of pre-orders if a company is going to limit how many can be made total.
Another option for Nintendo, maybe sell a digital pack of villagers through their eshop, though not ideal, at least people aren't blocked from their favorite villager just becaues Nintendo refuses to do a pre-order even that isn't limited by a number. Plus it wouldn't cost Nintendo any production cost selling a digital pack. Maybe it could be connected to your Nintendo account so it could somehow be transferred to other future digital AC games.
This is one of my frustrations with Nintendo lately, it is almost like they are handing stuff over to scalpers. I just know, Nintendo lately has been losing my money because of frustrations I have been having with them for a while. And I am sure I am not the only one. So many people are willing to purchase amiibos.