The GameCube era was weird because they had this 'seasonal' content idea planned out to bolster their line-up and keep development time manageable as well as take into account the limited space of GameCube disks.
Nintendo had also done research on how many people finished their biggest N64 titles and they discovered that only a small percentage of players had completed games like Mario 64 or Zelda OOT.
Most games were supposed to have direct sequels using mostly the same assets. That's why some GameCube games like Pikmin were very short. It was meant to get a sequel within a year.
They had sequels planned for the early line-up (Wind Waker 2, Pikmin 2, Metroid Prime '1.5', Rogue Leader II etc.).
But most of those became bigger projects or were scrapped in favor of 'real' sequels after their shorter games (Luigi's Mansion, Pikmin etc.) weren't received well by the public.