What Could Have Been: The game started out as a game called "Adam and Eve" which focused on their lives. The game was set in a prehistoric environment (mammoths and all) where you would watch the life of two characters unfold and eventually the amount of characters would expand. You were originally in a "God" role, mainly watching the characters and making them either fight or giving them love. The idea was scrapped because they couldn't figure out an objective for the game.
Originally Pikmin didn't have a protagonist and the characters were weapons shot by the player. Eventually the Pikmin were changed into being more like companions and tools, and Olimar was created.
The Pikmin themselves had several design changes. They were first around the size of a house cat but were made smaller later in development. The original design was completely black with no facial features. Later on they were changed to be pastel colors but the final product uses just red, blue and yellow. The Pikmin were originally meant to be different shapes (fat, tall, short, thin, etc) and they each had their own life meters but it was deemed too complicated so they opted for one size of Pikmin in three different colors.
In Pikmin 3 there was an unused character◊. He was scrapped due to complications with using 4captains.