Part of the problem are the parents who raise their kids to be spoiled, entitled assholes.

"BUT MOMMMMMMMMMMM, I HAAAAAAAAAAAAAVE TO HAVE TEH NINTENDOS!!!1" "Okay Timmy, I'm gonna go wait in line for hours instead of spending time with you. Or shell 2-4 times as much to buy one from some scalper."

Limited stock isn't a problem; consumerism and a lack of patience is. It's not like this is a rare item; it's just rare for the moment. Look at the original Wii. If you didn't have a pre-order, you didn't have one on opening day. Months and months later, they were still hard to come by. Now? Literally $40 at Gamestop for a used one. Low production numbers don't mean a damn thing if your mentality isn't "OMG I NEED THIS RIGHT NOWWWW". Production numbers aren't the problem. People are.

Different Nintendo topic: 11% stock drop after the release of Mario Run. Yikes.

Here's where they royally fucked up that release:
-Announce title in huge press event that spreads like wildfire
-In much smaller announcement weeks later, announce "oh by the way it'll be $10" that only Nintendo fanboys really take notice of
-Weeks later, release game "free" at the App Store, only to be told after three levels that it's $10 to unlock the rest of the game.

See, consumers either knew and forgot about the price, or were duped by suddenly seeing it at no cost in the App Store and understandably thought "oh, maybe they've released it for free or made it a holiday special or something". Nope, Nintendo and/or Apple simply pulled a bait and switch. But there was such an immensely easy fix that would have saved so much of the complaining:

Release a goddamn demo version. Two apps in the store: Mario Run DEMO, and Mario Run. Now there's no way in hell that people will be confused when they're abruptly asked for money after getting a taste for the game, and most of the complaints will now be based solely on the personal opinion of whether or not the game is worth the price.