Third-party publishers and developers don't care if flagship first-party games out-sell their own offerings. That's a rationalization made up by some Nintendo fans to soothe their own bruised egos.
What third party publishers and developers care about is the return on their investment and the long-term viability of a platform to demonstrate market growth.
I think they're fine with Zelda or Mario doing big numbers. Those games are system-sellers, which help expand the user-base. However, they're also looking at a limited attach-rate. Zelda/Mario at the top is fine but when the rest is rounded out with Mario Party or Star Fox, then there is a problem with the market either being bound to the "Nintendo" brand or pre-disposed to a certain aesthetic that does not favor most third-party franchises.
If that's the case, then it would require a lot of money and effort to re-position the market. It would require co-operation from Nintendo and all the major third-party publishers and even then it still might not be worth the investment.
