Here's what I think basically has happened ...
Once upon a time there were Nintendo fans. And sure a lot of them fixated on Mario/Zelda/DK/Pokemon but there was also a large enough portion of them that bought a fairly wide variety of games. Even on the N64, they'd be willing to buy things like GoldenEye, F-Zero, Star Fox the WCW games, Turok, South Park, Killer Instinct, Star Wars, San Fransisco Rush, Top Gear Rally, NFL Quarterback Club, Perfect Dark, Wave Race, 1080 Snowboarding -- as in Nintendo and third IP without Mario/Link/DK/Pikachu in them.
Then what happened is as the 2000s went along this ... this "diverse" portion of Nintendo fans started to splinter off. Some of them became disillusioned with Nintendo's direction with the GameCube and Wii and opted to become Sony/MS fans. To be honest some of the erosion actually began in the N64 era when a lot of people realized the N64 was no SNES-2. These fans have never really come back. They may have bought a Wii as a secondary party console, but they don't use it as their main machine for core games.
What you have now is a very different breed of Nintendo fan. They are the remaining group that fixates on Mario/Zelda/Pokemon/DK/Mario Kart/Smash like they have tunnel vision. They won't even support Nintendo IP like Xenoblade or Star Fox or F-Zero or Wonderful 101 any more in very large numbers, so Nintendo has resorted to overusing Mario.
In this environment, third parties don't have a prayer. The Nintendo fan that was willing to give games like 1080 Snowboarding, Turok, and F-Zero a shot has completely left Nintendo.
I meet many hardcore Call of Duty/Battlefield fanatics who'll exclaim that GoldenEye was the game that got them into the genre.