Like every game around the world, The President's Adventure did have beta elements involved in it's creation and further more. Here's a list and a short explanation for deleted content or/and never used content.
Right at the beginning of the game, one of the main breakout ideas will be the possibility to customize your Pikmin. First, it would have been a single Pikmin customization. Later, it start being one customization for one Pikmin color. Later then, it was deleted.
Reason: customization was removed from the gameplay due to take attention from the main story. Being a strategy and action game, customizing Pikmin with funny hats and clothes might be nice and funny, but was removed definitely.
Also right at the beginning of the game, one of the main breakout ideas will be the possibility of Pikmin to have jobs. Those jobs will only change the Pikmin status, like making it's jump go up and speed go down, something like this. Thirty five jobs where created into a existing page in the wiki. Click here President's Adventure/Pikmin Jobs to see it. Some time after, it was deleted.
Reason: There where too many jobs, what will make the game heavy. Also, it would bring the need to create a status for Pikmin, what Nintendo should have done in one of the canon games. Since The President's Adventure is a beginner fanon game, doing such important thing will be a hell of a job. For that reason, Jobs where excluded from the gameplay.
To fully complete the Challenge Mode, three sets with four caves each where created as part of the Downloadable Content. Those caves never reach development phase, and, without any changes or thinking over, were deleted.
Reason: The game is filled with caves and levels, plus the Challenge Mode, with is a full pack. There was no need for more caves, such as the Downloadable Content. For that case, it was removed.
The First Story
The game had two different stories. The actual, the one who's the official and the previously one, who told about The President's special Pikmin partner, Partner. That story was deleted and left behind, then, replaced by a much simpler and understandable one.
Reason: The story was too complex. The game was actually kind of better when replaced with a much simpler story.