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TheRealSamusAran said:

It warms my heart every time I see Metroid still being called one of the three elite Nintendo franchises even though it has never been a heavy seller like the other two. And it shocks me that I didn't see Pokémon mentioned once on the first page. If we're talking of franchises, I think that one takes the crown easily, if we're talking of a single game, it gets trickier. I think I will stick with Pokémon and say Stadium is the best Nintendo game not from the Big 3.
Gosh, that was a hard question.

Metroid may not be one of the best selling Nintendo franchises, but it's definitely one of the most prestigious, with Super Metroid and Metroid Prime featuring high on almost every list of best Nintendo games.