During development, a lot of elements, enemies, features and characters were added/removed before the game was actually defined. Here's some of the things that were meant to be in the game, but, for some reason, were removed.
A new kind of Pikmin. Nothing was really known about him, his abilities or way to breed. Everything was undercover. Before it's final thought, nothing were revealed and his appearance were excluded.
Reason: There was already three types of new Pikmin. It's presence will be obsolete.
Lilith and Dark Lilith
Two enemies that have their bodies made out of tentacles. They were removed, for a still unknown reason. Their only appearance was in the first Beta Gameplay, but too little were revealed to make them "a sure deal" for the game.
In the Beta Gameplay, all the enemies listed below made an appearance. Due to the video being a Beta Gameplay, they're appearance is not confirmed in the game, therefore, turning them into Beta Elements.
A purple body Bulborb with a space helmet. During Beta Gameplay, Space Bulborb's behavior showed a little agressive, and attacked The President in a rocky like area (supposed being the Moon Bounce area), but was defeated by Red Pikmin and the Space Pikmin, who was Red Pikmin wearing a space helmet.
Still in Beta Gameplay, while walking in a rocky like area (also supposed being the Moon Bounce area), a dark purple clone of The President appeared. The cosmic clone looked a lot like those clones present in the Super Mario Galaxy series. Using Pikmin was enough to defeat it, which gave the player a treasure, being the Cosmic Clone a possibility of boss.
During Beta Gameplay, The President fight a shinying Bulborb, who looks a lot like the common Bulborb. After being defeated, it gave seeds that sprouted the Gold Pikmin. However, being the Beta Gameplay video, it's possible that Golden Bulborb won't be included or that he won't have the power to gave out Gold Pikmin seeds. Also, he's name's not confirmed.
A confirmed enemy that will be the boss of the Beetle Jungle cave. It looks like a Iridescent Flint Beetle, but it's huge and cover almost the entire screen. It isn't as fast as the Iridescent Flint Beetle, and it don't move, just turn his body to spot the player and the Pikmin. He's a confirmed boss in the game.
An insect like specie of the Chomp Chomp, enemy from the Super Mario series. During Beta Gameplay, it chased the player and eated Pikmin. Instead of the metal chain it has tied to his body, the Chompy Chomp, which is pink, has flowers. Also, during a quick scene from the Beta Gameplay, the Chompy Chomp was tied to a three, tried to attack The President, but couldn't.
A supposed enemy from the game who looks like Winnie, the Pooh. It is smaller and looks more like a toy bear, with button eyes and a tied up mouth. During Beta Gameplay, it was attacking a three with a hole in the middle. Supposably looking for honey. It didn't attacked The President even when it walked very closed to it. It's body it's all yellow and it wears a letter vest.
Arcana (supposed name)
During Beta Gameplay, it was spotted a light blue energy walking creature. It looked like made of ice, because it left a trail from where it walked. Few things are known about this creature, which wasn't even interected with in the Beta Gameplay.
Another confirmed enemy is supposed to appear in levels where snows. It is a frog with red cheeks and a snow looking like body. In the Beta Gameplay, in a level with snow, still unknown, the Frogbert opened his mouth and spitted a giant snow ball, that killed several Blue Pikmin. When it was defeated, it gave away a treasure, what gives the possibility of him being a boss.
A confirmed boss from the game. It is unknown in what cave or area it will appear, and it's skills and battle formation is still unknown, but it is definitely going to appear.