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Illusion said:

Some additional franchises that I thought of:

SNES: Yoshi's Island (Yoshi's Story, Woolly World, Crafted World series)
N64: Pokemon Snap (N64, Switch), Pokemon Stadium (Coliseum)
Wii U: Super Mario Maker (this and Splatoon were major innovation from Nintendo, imo, during the Wii U era)

From a commercial success perspective, Pokemon has really been Nintendo's biggest new-IP find since the NES days. While this started on a handheld, the N64 was really the first home console that saw Pokemon games and it did get a lot of them and so I will give N64 the Pokemon prize for the purposes of this thread. Smash Bros is probably #3 on the list for new IPs in terms of popularity post-NES after Pokemon and Mario Kart and so I will have to say that the N64 is the overall winner here.

It's a tough question though because the SNES had so many franchises that started on the NES but rose to fame in a major way on the SNES (Mother, Final Fantasy, Metroid), it just seems unfair to give all the glory to the NES for these franchises.

Almost every first party franchise was bigger on the NES than on the SNES.  Mario, Zelda, Metroid, Punch Out, etc... were all more popular on the NES (i.e. sold better).  Mother only made it out of Japan on the SNES, but it had disappointing sales.  The notable first party games on the SNES were either bigger on the NES or brand new series (Mario Kart, DKC).

Third party games are a different story though.  Third party games often were more successful on the SNES.  Final Fantasy is a good example.  (Although PS1 Final Fantasy was far more popular than SNES Final Fantasy.)