God Never Said That: Some people are flat out convinced that Yoshio Sakamoto considers the Prime Trilogy not part of the canon, when in reality they are merely stated to be side-stories and are still canonical.
What Could Have Been: In Corruption, the starship was originally meant to play a larger part in the game, with piloting sections. Sadly they were cut, though this does explain the otherwise pointless missile expansions you can get for it.
Multiplayer was going to be expanded/fixed for Corruption, based on improvements from Echoes and Hunters. Retro Studios ran out of time.
A design document for a "Metroid 1.5" was leaked in February 2011 detailing what would have been an alternate sequel to the first Prime. In it, Samus would have been trapped on an alien starship from another dimension immediately after the first game. The aliens who owned the ship would be capturing bounty hunters from across the galaxy in order to assimilate their powers. There also would have been hybrid mixes between the aliens and Space Pirates or Metroids. One in particular, the Humetroid, a human/Metroid hybrid, was designed as a scout; a Metroid carried on its body would go out in advance to scout an area, while the "body" remained invisible.. There also would have been a ship AI that had four components, some helping you, others fighting against you. Unlocking abilities would be done by deactivating the barriers to them on the ship, but doing so would eventually lead to the creation of an evil doppelganger Samus. The ship would have been as big as the Phazon Mines and Chozo Ruins combined and would have featured many more puzzles. The game also would have featured multiplayer much deeper than either Echoes or Hunters. The concept never fully got off the ground, but several elements (multiplayer, evil Samus doppelganger, alien villains from another dimension, ship adventure with unconventional method of unlocking abilities) were salvaged and later used in the other Prime games and Other M.
Kraid was reportedly going to be a boss in the Phazon Mines in the first Prime game. The only remaining image of him is this render.◊