Nintendo didn't get stomped in the N64, Game Boy Color generation. They had tons of awesome games on both.
Gamecube got stomped though. Third parties didn't want to develop for Gamecube because it was perceived as a system 'for kids' and you had to change the format to make the game on mini-discs. Plus, some of Nintendo's first party efforts weren't that great. Mario Kart was the worst Mario Kart ever, or one of the worst, Super Mario Sunshine is the worst 3-D Mario by far, and people whined about Wind Waker's graphics, even though the game was awesome. The system was hardly for kids with Metroid Prime, Eternal Darkness, and Resident Evil 4 on it, though, all of which were awesome...
GBA helped though, Nintendo had the monopoly and third parties didn't mind developing for it.
See, as said, I think third parties hold Nintendo back more than Nintendo itself.
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