The Metroid franchise has seen its share of cancelled games and scuttled concepts:
Not only was there a full-color version of Metroid II: Return of Samus planned for the Game Boy Color (that was apparently scrapped very late in development), but Retro Studios also considered remaking it at one point as a side project.
Samus' death animation in Super Metroid was going to be a little more mature - when the suit exploded, she was supposed to have been naked and would have screamed. However, the developers felt that went way too far, removed the scream and painted over Samus' body with something of a swimsuit.
There were discussions about possibly making a "Metroid 64" for the Nintendo 64, but production never got any further than a few vague pie-in-the-sky ideas. According to one interview by Yoshio Sakamoto, Nintendo approached at least one company with a concept - said company turned it down due to fears that it couldn't live up toSuper Metroid's standards.
An early prototype of the game was developed for the Nintendo Gamecube, and was intended to have (among other things) a third-person perspective, a different character model for Samus, no loading buffers and a different HUD. The prototype was all but scrapped by Shigeru Miyamoto after its public debut at Spaceworld 2000, ostensibly because controlling in third-person was too difficult, and the game was reworked to use a first-person perspective.
There was intended to be another boss in the game - Meta-Kraid. The design of the character got far enough that he was modeled and skinned, but time constraints prevented him from being included in the final version. (The developers claim that the beta model◊ was not replaced by the Omega Pirate, despite the model shown in the boss arena from the Phazon Mines.) Likewise, an early version of the Ripper was also intended to be in the game, but was also scrapped.
Samus was originally intended to be voiced (by Jennifer Hale, no less), but this was scrapped and Samus remained mute for the duration of the game. The only hint of this narration is an alternate opening sequence that is still present on the game files, where Samus narrates her experiences up to the beginning of the game.
Another What Could Have Been comes from all the games Nintendo cancelled so Retro would only focus on that game (including the RPG Raven Blade, which could fill a gap in the GameCube's library of said genre). Additionally, all of the Prime games have unlockable concept art, which contains many different designs and concepts, though opinions differ on what would have been better or worse.
Prime 2: Echoes:
Early plans for Echoes were very different from the final game. An early pitch document, written by level designer Tony Giovannini, detailed possible ideas for the game, and included unused gameplay/design elements like aliens in cryostasis, a schizophrenic AI, a gameplay mechanic where time can flow backwards and/or the gravity of a room can be altered, many different enemy types, plans for a an "Ancient Chozo Robot Battle" multiplayer mode (where the players roll up into the chestplate of ancient robots and use them to battle) and much, much more.
There was a plan to have both Dark Ridley and a Dark Luminoth enemy. The latter was scrapped because it made no sense in-story; a Luminoth would rather self-terminate than allow itself to be controlled by the Ing.
Prime 3: Corruption:
Corruption would have used Samus' gunship a lot more. The final game is still full of Gunship Missile Capacity Upgrades and Gunship Missile Refills, but due to the rarity of doing bombing runs in the game, they're very nearly useless.
The game was also planned to have a multiplayer mode and it would have been more fleshed out and developed compared to the bare-bones multiplayer found in Echoes. The concept was scrapped due to time constraints.
The early beta for Metroid: Fusion was very different compared to the end product. The beta (which premiered in 2001 at E3, and was planned for the Game Boy Color) had a alternate stylized logo (called "Metroid IV"), a different Fusion Suit for Samus (which she seems to have voluntarily put on, if the short cutscene is any indication), Metroids could be encountered outside of the Research Laboratory, there were additional suit upgrades (one of which allowed Samus to tether enemies, and another which allowed her to walk on walls) and a different ship layout, possibly among other changes.