Thanks for linking (and providing handy bullet points!).
But I'm not sure if selling through their own website is enough. I mean, the craze is real. Nintendo couldn't keep Club Nintendo from crashing on the last day to register codes despite ample notice and about as wide a time frame as you could get. (Admittedly, I was one of the people who procrastinated and contributed to that problem.) I just have no faith that Nintendo could keep it's own site open.
Plus, Nintendo's only friends right now are retailers (maybe). Boxing them out of this deal would probably put a bad taste in their mouths. I don't think the retailer exclusives were a point of laziness on Nintendo's part, but rather an agreement to ensure shelf space.
Further, imposing the limit is easier said than done. Apple does this with iPhones by scanning an ID. That works with in-store transactions that they fully control. Nintendo wouldn't have this luxury online and would instead have to rely on someone (or some expensive software) to go through transactions to make sure credit cards are being used more than once, billing addresses aren't being used more than once, shipping addresses aren't being used more than once, AND that none of those would produce a false positive (e.g., two people living in the same house ordering the same Amiibo).
Great points, in theory, but they just don't seem practical.