I think you hit it right in the mark about amiibos. As popular as Nintendo characters and their respective IPs are, it was probably hard to gauge their potential popularity upon release with amiibos, especially during a time when the 3DS and the Wii U were selling below the rates of their respective predecessor's. Wihle toys-to-life was still popular at the time, it's not too long ago they faced a decline. I don't know any numbers right now, but I don't think the sales are as big as they used to be 3-5 years ago.

As for the NES Classic Mini, it probably was inexcusable sell low productions. Due to the nostalgia, there's still a huge craze for retro gaming and the NES Classic was a big deal, especially at the $60 price tag it had. There's a possibility it discontinued due to having similar chips and parts to the Switch so Nintendo had to put more focus on the Switch, obviously, since its the new console and part of their bigger investments while the NES Classic was meant to be more of a smaller but still popular thing.

I am going to be clear. I am was never trying to downplay the Switch success. I really like Nintendo and will be getting a Switch at a later point. If Nintendo does this or not I am not bothered anyway. Switch is great. I enjoyed the Wii.

No, it's a stupid notion.
They would only benefit from supply manipulation, if they have incredibly high profit margins. Or if they are in control of their market, a market leader or monopoly.
Also, people should keep in mind Nintendo is a public company with shareholders to please. And they judge Nintendo's performance quarterly. I don't know if Nintendo said anything about supply to shareholders, but Nintendo can't purposely lie about their business to shareholders. If they say they have supply issues, it is mostly true, unless if they wanna risk getting sued.

Miyamoto is probably hiding some of the stock in his basement.

What if Nintendo is just terrible at estimating demand for their products?

2 to 4 units does seem like very few but if you've got a limited amount and are trying to spread it out across the thousands of stores across the US. I can see it as possible that your store got so few units.

I'd argue that Black Friday is definitely  a day where they don't want to be undersupplied. You've got tons of busy parents doing their holiday shopping, they don't want to come back another day so if they don't find a Switch many of them with go with an alternative, be it another console or something else entirely (to the dismay of their kid).

Did the Wii U ever have stock issues?

Your analogy is terrible but I get your point nontheless. I thought about leaving it open ended but it wouldn't have given my the answers I was looking for. In the end, my proposition wasn't that extreme since they are users who responded affirmatively to it and provided their own reasoning for it which is what I was interested in.

No. The idea itself is pure BS. Nintendo needs to gain a large installbase ASAP to maintain maximum profitability now that they will only rely on one device. The more the bad supply lasts, the more potential customers they might loose. Simple as that.

Nintendo doesn't want to create the image of a highly-desirable product by enacting shortages, they want to be the go-to gaming device that anyone can pick up as soon as they want and start buying games for it.

nobody with basic business understanding would seriously suggest that the artificial shortages are a thing. The only way it could benefit a business is if it was done in an extremely marginal way; i.e. providing very SLIGHT amount less than demand as to maintain a fake hype.

Unfortunately if you're in a scenario where you're providing a fraction of the amount of systems in relation to demand- it provides extremely limited benefits. It stops/prevents larger software sales (the bread and butter of the industry), and potentially results in somewhat bad PR for a business (threads exactly like this which suggest the company is not necessarily looking out for their customers).

Beyond a business perspective- there is a lot of background talk recently with the scarcity of certain components for mobile electronic devices; only a few companies are currently making extremely high end parts and the resources used to create these are highly limited. when you're competing with Apple or Google for manufacturers- well there really is NO competition. You just wait your turn. That's where Nintendo is at currently.

Again, artificial scarcity only makes sense when marginally done to build a bit of hype while maintaining solid sales. If you're providing a fraction of the systems that could potentially sell then that's just suicidal as a company like Nintendo certainly wants high revenue ASAP because that's what funds future development of games (its a circular thing).

Artificial shortages also are somewhat illogical on really hot products. Something like the Switch is useless to deliberately undersupply because it has great word of mouth currently and is pretty positive online. IF this was a Wii U scenario where the initial allotment had taken a while to sell and was doing mediocre- undersupplying might make sense to be safe and to potentially make people want something they can't get it (although rarely does that actually work because in the end the demand is there or it's not, regardless of supply). 

In the end we have an awkward combination of Nintendo likely being conservative going into this generation after what happening with the Wii U's initial gigantic first week supply sitting in stores for months- and a difficulty with the top manufacturers of specific parts that the Switch and other mobile devices use and have in common.

I don't think what has happened is rocket science and the artificial scarcity stuff is just absurd and generally has not explanation in theory. It's like the people who claimed the NES Classic was deliberately being undersupplied despite the demand. Ehrm... yeah... Nintendo undersupplied the system to build hype and then just discontinued it entirely when they don't appear to have plans for Virtual Console anytime soon on the Switch. The point being that there was no scarcity ploy, and that people just give frustrated and come up with asinine theories.

Nintendo misread how well the Switch would do (as did many people online), and happened to decide to try to boost supply in an awkward period of time where there is high demand for the same parts for different electronics. That's all 

Nintendo has actually fairly rarely had stocking problems; people way overhype things. The reality is there are certain regions that it will always be hard to stock well for compared to others. The only time I can even think of where the theory potentially has slight grounds would be the Wii era, but even then they were manufacturing LOADS of DS's at the time, so it's not hard to imagine that it was somewhat difficult for them to manufacture for home consoles and handhelds at a quick enough rate.

the fact that there is a shortage in high end parts for mobile electronics at the moment adds to the difficult in manufacturing (google if you haven't heard about the issues, the Switch uses a few of the the same high-in-demand parts that things like Apple phones also use)

I'm pretty sure skalpers account for less than 0.5% of the market.