No, the retailers. What would Nintendo have to do with scalpers? The only place that Nintendo would have any control over that is at the Nintendo story in NY. 

Actually, it makes sense for any producer of any product to err on the lesser side than flooding the market. Same reason that the PS4 was short supply or any other console that has went through the same thing. Or any product that is harder to keep the stock levels under control really. Part of it is planned without doubt, but they are in the market to make money, not to drive up prices that in no way helps them sell more product lol. They would have produced more of what they thought was going to sell more and less of what they thought was going to sell less. 

For production like this, there is often a waiting period, especially when they already have other lines predetermined. Production companies and production lines almost always have waiting lists so much of this stuff is ordered a year ahead. There are certainly exceptions though, like if a certain production company that only produces something specific and there is less demand for it. It likely took a lot of extra money to create a second line for Marth in such a short time, but that is likely why it's only Marth instead of more of the rare characters. 

They might be worried about bursting the bubble. It's hard to tell how big the bubble is when scalpers are so rampant and retailers aren't doing anything to control the situation, or at least, more of them aren't. It's basically a false bubble, but it would be a major loss in revenue if they were to flood the market because of all the extra stock sitting on store shelves and likely in boxes at the distributers... 

Part of my job entails warehousing, I don't deal directly with it, but a very good friend of mine does and I am being trained in it due to my role/position and I have learned a bit of what all this entails. What the Nintendo rep said is very true. 

Well, my friend and I were trying to get a Ness Amiibo at the same time. We waited...and waited... but the Gamestop site crashed. A few days later, he asks me if I got the Ness amiibo, I said no but he said "that he did". He said that he went into gamestop and pre ordered it in store. He proceeded to tell me that the new wave never went on sale for online pre orders...

...

Ya, the popular ones they keep in stock, a.k.a Mario, Link, Pikachu, Luigi, Donkey Kong, Kirby

How often have you seen a Villager or a Pit amiibo in a store?

The retailers definitely make the issue bigger, but they're not doing anything they wouldn't normally do.

It's Nintendo's fault.

You've hit the nail on the head there.