Gameplay-wise, the game was originally going to have a lot of the features that Metal Gear Solid 2: Sons of Liberty had such as dragging bodies and hiding in lockers but weren't implemented in the final version. It was also going to have music that would change throughout different areas.
Decoy Octopus was said to have a battle planned similar to Laughing Octopus in Metal Gear Solid 4. Also, Sniper Wolf was originally conceived as a male character before a re-imagining as female. Concept art still exists of her original design.
Solid Snake was also going to have strings coming from his bandana. Because it was hard to animate these strings on the original PlayStation's hardware, his bandana had to be a generic headband. However, they were able to pull it off in later games (even on Metal Gear: Ghost Babel, since that game used sprites).
The Metal Gear Mk II (later implemented in Metal Gear Solid 4) was going to be one of Snake's gadgets. Demo footage exists showing it in the inventory.
Shadow Moses Project, a fan made HD remake of the game in Unreal Engine 4, was cancelled in 2016, probably due to licensing.
Metal Gear Solid 2 originally made even less sense. Rosemary was supposed to be a hostage on the Big Shell itself, who would constantly be moved as Raiden would go to rescue her, leading the player to doubt her existence. Pliskin would have been blond and worn a crucifix, Snake and Otacon would use their real names when alone together to suggest at their intimacy, Johnny Sasaki would have served the role Richard Ames does and had a Heroic Sacrifice, three characters named for characters in Paul Auster's New York Trilogy would have been Raiden's support (they would all have turned out to be AIs, as Raiden's support in the released game ended up being), and Fortune would have been a saxophonist slowly dying a blood condition (which would be treated by the originally female Vamp sucking her blood erotically). Most famously, a few bosses were cut, including two extra Dead Cell members — Old Boy, a hundred-year-old soldier and Big Boss's old trainer (recycled as The End and The Boss in Metal Gear Solid 3) was instantly taken out, but Chinaman, a Vietnamese swimmer and illusionist, stuck around long enough to have a boss battle arena built for him. His powers and that boss arena were eventually given to Vamp, and he got a small cameo appearance as the dead man with the long dark hair in Fortune's arms during a flashback. Bizarrely, the Metal Gear Solid 3 character The Fear was based on Raiden's original (and instantly rejected with extreme prejudice) design.
Another fight cut from the game was to take place in the Shell 1 core's computer room, where the player would have defended Snake as he attempted to tend to Emma's wounds after crossing the oil fence. The penultimate Metal Gear Marathon Boss fight was also changed - originally, Sergei Gurlukovich was supposed to survive the events of the Tanker chapter, only dying just before the Metal Gear fight, which would have been Solidus and Ocelot in a pair of manned RAYs versus the player and Gurlukovich's remaining soldiers attempting to avenge him.
The trailers (and a flashback from Snake) show a scene of Snake outrunning the flood in the sinking tanker, but that was cut at the last minute because the actual gameplay was incredibly boring.
Before the New York Trilogy turned MGS2 into a huge mind screw, the original plot would have revolved around a typical terrorist-hijacked tanker.
The first draft was going to be set in the Middle East, with Snake fighting Liquid (who had faked his death and stolen some warheads). This setting was immediately abandoned when the Middle East conflict at the time began to heat up, making the plot tasteless.
The game was also going to have Arsenal Gear crash into the Twin Towers, and have the Statue of Liberty be moved to a different part of NY. In the middle of the credits, it was going to show a news report of the Statue of Liberty's relocation, instead of the live-action clips of NYC. The script for the news report can be viewed in The Document of Metal Gear Solid 2. It was also going to have Raiden cut the rope from an American flag and drop it on Solidus's dead body after defeating him. All of these things were cut once September 11th occurred, although most of them were reinstated eight years later with the release of the novelization.
Under the same reasons as above, it was also intended for Liquid Ocelot to crash Arsenal Gear into Manhattan, and that Vamp explicitly state that Dead Cell intended to launch the nuke directly at Manhattan instead of letting Solidus black out Manhattan via an EMP wave, but were cut (although it too was retained in the novelization).
They thought of including a mask called the "Mantis Mask" based upon Psycho Mantis in the game, that allowed the player to read the thoughts of other characters. It never made it into the final version, though the concept may have been recycled by way of the secret messages occasionally heard with the directional microphone.
Metal Gear Solid 4: Guns of the Patriots nearly ended with Snake and Otacon turning themselves in to the authorities and being dual-executed for their terrorist actions. It was changed when the staff flat-out mutinied. The final song, about a pair of anarchists executed unfairly, remains as a monument to the original ending.
For a while, the BB Corp would have been naked when shedding their suits, but Hideo Kojima realized the game would have slapped with an AO rating. And there would have been two male BB-like characters who served a similar, Gender FlippedFan Disservice role - "Snake-Man", a beautiful young man with tentacles coming out of his body, and "ADAM", a handsome Russian soldier.
In terms of play mechanics, MGS4 was supposed to be more complex and have less Metal Gear-isms. Kojima talked in early interview that Snake could choose sides if he wanted in any of the conflicts (think Mercenaries), even mentioning times when Gekkos would ignore or even help you. There were supposed to be less visual cues like the exclamation point over an enemies head as you were supposed to be able to tell from their facial expressions and mannerisms. There were also elements of psychological warfare such as enemies who spotted you would threaten you instead of always trying to kill you. Some of these features made it into the game, but in a cut-down form - in particular, it's possible to befriend the local resistance movements in the first two chapters to gain their help, but PMC soldiers and their unmanned support invariably shoot the player on sight.
The OctoCamo mechanic was rather toned down from their original intent - they were hoping it could mimic moving objects like running water, rather than just switching flat textures, but attempts to do so would have taken more processing power than the PlayStation 3 was capable of.
In addition, according to Kaz Radio and other sources, MGS4 was originally not going to happen, with the series chronologically ending at 2, and release-order ending at 3, which also would have caused some problems since MGS2 ended on a cliffhanger. Thankfully, saner heads prevailed when MGS4 was greenlit.
Metal Gear Solid 3's The End fight would have been a much longer cat-and-mouse, track-over-several days ordeal, as Kojima was inspired by an author's series of novels in which two snipers try to track each other. This was changed when it got too long and the staff literally booed him.
The End was originally going to be called "The Doom", but this idea was dropped due to Doom 3 coming out around the same time.
In terms of play mechanics, Metal Gear Solid 3 was to be an open-ended game in a huge connected jungle, with a night and day cycle and dynamic weather.
Originally, the ability to free-roam and set traps such as snares and tiger pits were planned, but the system couldn't handle the programming.
The scene where Sokolov and Snake apparently speak Russian in Japanese or English is a remnant from when the game was intended to have the characters actually speak Russian across the game. This was dropped because the cast, save for Snake's Japanese actor Akio Ohtsuka, was unwilling to go through the effort of learning Russian.
The fight against the Shagohod was originally supposed to have an entirely separate form that acted as an escape pod that they had to destroy, but it was removed from the final version and instead replaced with Volgin controlling the remains of the Shagohod through its wiring.
A beta trailer depicts Solid Snake traveling through the jungle instead of Naked Snake/Big Boss, but this was likely just a placeholder.
The game was originally going to be on the PS3, but since that console's development took longer than expected, the game was put on the PS2 instead.
Tiger Toys was planning a portable version of Metal Gear Solid for their short-lived portable platform Game.com. Thankfully it was cancelled, because every game ported to that console was a Porting Disaster of epic proportions.
Revengeance was originally going to be titled Metal Gear Solid: Rising, and was set to take place between MGS2 and MGS4. It was also set for a Play Station Vita release as well as PS3, 360, and PC. But when Kojima couldn't get the gameplay to work just right, development was continued by Platinum Games, who moved the story four years after the events of MGS4, but is about Raiden coming to terms with his past and reverting back to his "Jack the Ripper" persona. Also, the PS Vita version has been cancelled.
Early enemies from the game showed a strong Psychological Horror vibe similar to Metal Gear Solid 4's designs, such as unmanned robots holding weapons that resemble a tall, distorted woman breastfeeding a baby. The eventual game was much more Rule of Cool and less psychological in tone.
Early previews showed players would invade one another's Mother Base. This was changed to invading forward operating bases instead, which basically function the same way. Previews also suggested enemy forces could randomly invade in single-player, but this only happens once, as part of the FOB tutorial.
Mother Base was shown to be much more alive in an early gameplay preview, showing things such as UAVs (which only appear in FOBs in the released game), animals on the main base platform (instead, they have their own conservation platform the player has to travel to), a gun range the player can visit (only appears as part of one cutscene), and Ocelot hanging around and saluting Snake (only appears on Mother Base outside of cutscenes as part of a tutorial mission and to tell Snake about Quiet's condition).
Previews mentioned being able to call for supply drops of animals that the player has rescued and using them to wreak havoc on enemy bases.
An early gameplay trailer showed "Cooperation" on the iDroid menu, suggesting co-op multiplayer like Peace Walker was intended at some point in development.
The game was originally meant to open up to "Diamond Dogs" by David Bowie. It instead opens up to a Midge Ure cover of "The Man Who Sold the World".
The Collector's Edition bonus disc has a feature called "Phantom Episode/Episode 51", which details a key story mission that was cut for unknown reasons during development. After Eli/Liquid and the child soldiers steal Sahelanthropus and flee Mother Base near the end of the game, Snake and his allies would have had to assault his stronghold on a remote island in Africa. The mission would have ended with most of the children dying, Eli being left by Snake to die on the island, and Mantis/Tretij Rebenok rescuing Eli (and removing his vocal parasite) before the island is napalmed.
Concept art from the official book explains why Chico's death feels like such an afterthought. It was originally planned that instead of actually dying, Chico would've been horribly disfigured in the crash, similar in manner to Skull Face, and to have gone insane in the years between games, growing up to be a masked killer with an Oni-like outfit. Additionally, lines that had been recorded and dug up from code, indicate he would possibly be a buddy, similar to Quiet or D-Dog.