Frankly, it has a lot to do with them being Nintendo games... looking at their consoles so far:
NES: Hugely collectible, largely spurred on by giant retro-gaming presence on youtube
SNES: Same as above
N64: A few years ago kids who grew up with this system began to become young adults with expendable cash, and this age group tends to be the one who really drive those prices up
GC: While relative scarcity played some role in the N64's prices (compared to the PS1), scarcity had a far larger impact on the GC, which sold far less than the PS2. Add in that its games have largely aged the best of that generation (around the Xbox's hardware strength but with an art style that doesn't age nearly as quickly) and, much like the Dreamcast, it has seen its popularity continue to grow over the years. These games are continuing to get more expensive, then.
Wii: This is the one Nintendo system on which games are quite affordable these days. The console itself sold like hotcakes, and a large portion of those sales were to the more casual gamers who were happy to sell their games. I'm not sure this gen will ever see their games become too expensive due to an abundance of supply
Wii U: Unfortunately, there's two things working against this console that the previous ones did not have to deal with. First and foremost, while downloading games was a thing in the previous gen this was really the first gen we saw it become commonplace on a Nintendo platform, a reality Nintendo encouraged. This resulted in less physical media being produced (I never did get a physical copy of Wonderful 101), which was additionally troublesome as the initial production targets were much lower as a result of the second big issue: the console never caught on and fell 10 million short of their second least popular console (GC excluding Virtual Boy).
Finally, the tiny console sales also meant that a huge proportion of those who owned it were enthusiasts who were far less likely to part with their games, especially as those who made the effort to go get physical copies were even more likely to be the type that want to hang on to them for sentimental reasons. Essentially, then, it was the first Nintendo console to really limit physical media and rely on downloads, was only owned by a small number of people, and a larger than usual portion of those people were enthusiasts that would hold on to their games... so no, I don't believe Wii U games will ever be reasonably priced.
Switch: That brings us to the Switch, then, and really the combination of downloads being even more commonplace and the Switch itself being a huge hit makes it pretty unlikely we'll see prices drop much. It's generally third party games among more casual gamers that tend to see their prices plummet, but that just doesn't really apply to most Nintendo titles outside of the Wii's generation. Given the recently released demographics of who is buying the Switch, it seems quite likely that those who own physical copies of their games will be unlikely to return them for resale.
Of course, there's also nostalgic reasons for people to constantly buy up Nintendo games, with gamers having had relationships with these various franchises for decades now. In the end, though, it's one reason I'm so desperate for physical media to hang around, as otherwise games will be kept at bizarrely inflated prices without the option of physical media resales.
So, in short:
Supply/Demand
Nostalgia
Decades-old-franchises
(For some) low console sales
Prevalence of downloading games over physical media
Physical media being produced in lower quantities due to the above
