It's not an issue of them selling fast. It's an issue of Nintendo not knowing how to make a proper amount of stock for them. It doesn't help that pre-orders for it opened up in the middle of the day, when most people are at work, allowing scalpers to pick up a large majority of the copies. Then we factor in that places like Amazon don't limit pre-orders to one per customer. That paired up with the fact that Nintendo already under-stocks the Limited Editions, and we get the mess that we've seen with Fire Emblem Fates, Tokyo Mirage Sessions and now Fire Emblem Echoes.
Nintendo has always been awful at handling special editions, and unfortunately it's the fans that suffer for it. Especially considering that people need to pay $130+ for it now through a scalper.