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Some aspects of Pikmin 2 were only available in prototype versions, and have been changed or removed for the final release. This information is known from different sources, such as gameplay videos of earlier versions of the game.
Trailer
A trailer, seen here[dead link] shows little unused information, except for the fact that Blue Pikmin were able to enter the Lost Toy Box (this can be seen 50 seconds into the video).
Early Bulborbs
Two Bulborb subspecies are known to have been cut from the final versions of Pikmin 2, from analysis of gameplay videos and screenshots. These Bulborbs, along with the Red Bulborb, would have given each basic Pikmin type a Bulborb of the same color, had they not been removed. Naming used in the game's data makes it clear that these enemies eventually became the Dwarf Orange Bulborbs, Orange Bulborbs, Snow Bulborbs and Hairy Bulborbs in the final game.
A blue "dwarf" Bulborb is clearly seen in a gameplay video. It has white spots, and apparently acts like the Dwarf Red Bulborb, with the same health, attacks and weight. Its treasure value, however, appears to be 
× 5, whereas Dwarf Bulborbs are worth × 2 in the game's released version. An adult version was never shown. These blue enemies became the Dwarf Orange Bulborb – whose internal name is bluekochappy – and the Orange Bulborb – with the internal name bluechappy.
Yellow Bulborbs appeared in the same video as the blue one, but in an above-ground area that bears a striking resemblance to the Forest of Hope. A dwarf version was also seen, which seems to walk slower than other Dwarf Bulborbs. In the final game, Snow Bulborbs are internally called yellowkochappy and Hairy Bulborbs are called yellowchappy.
Prototype gameplay
There's an E3 2003 prototype gameplay video that shows yellow Bulborbs and slightly different cave entrance cutscene. It also contains several debugging elements: {{#ev:youtube|v=ssxpb_84KA0|350}}
This video shows an early version of the Challenge Mode. In this one, the mode develops in the Awakening Wood, making it very like the Challenge Mode from Pikmin, with the exception that the player is able to use sprays.
{{#ev:youtube|v=OKHpZGoz8eE|350}}