Defictionalization: Sony released a Bluetooth headset styled after Snake's Solid Eye around the game's release, which was even compatible with the game itself and could be used to listen to Codec calls.
Dummied Out: Otacon and Rose have Codec audio files for the Final Boss fight against Liquid which went unused, as the Codec cannot be activated during said battle.
Real-Life Relative: In the ending of the game, Solid Snake meets Big Boss once more. In the Japanese version, both characters are played by the father/son duo of Akio and Chikao Ohtsuka.
Talking to Himself: Averted. Being the first game since the MSX2 era to feature both, Solid Snake and the elder Big Boss, the latter's role is played by Richard Doyle, the voice of The Fury in the English version, and in the Japanese version by Chikao Otsuka, Akio Otsuka's real life father.
Torch the Franchise and Run: Hideo Kojima has always been open about the fact that he treated each installment after the original Metal Gear Solid as the last one in the series, hoping each time that it would bring the series to a conclusion, but this game is the most blatant about it, trying to portray basically everything in with a strong air of finality to it, giving an overall impression of the End of an Age. This is most notable with Snake himself, who due to his status as an unmodified human soldier is often referred to as being relic from a bygone age, and due to his accelerated ageing, he does not have much time left to live any way. This can easily be seen Kojima's attempt to prevent any direct sequels with Snake returning as the main character from ever being made, and indeed, Metal Gear Solid 4 is the final installment of the series with Solid Snake as the protagonist.
The game had a bigger emphasis on the factional warfare between the PMC and whatever rebellion is in the area, and the war aspect was more played up, with the war afflicting the environment - and thus, places to hide, such as tanks blowing out buildings or the vehicle you're hiding in being driven off to fight. Enemies didn't even sound an alert when spotting you - they shouted to inflict Psych damage.
In an "MGO Eyes" video, it was revealed that Metal Gear Online had three additional maps that did not make it into the game: the first being "Desert Duel," the second being a recreation of the Town stage from Metal Gear Solid: Portable Ops that was never officially named, and the third is "Lethal Leviathan," which was actually the ship bow of Outer Haven. The first and third were eventually added to the game's arcade version, Metal Gear Arcade.
Not from the game itself, but there was originally going to be more novels besides the novelization for this game written by Project Itoh. Obviously, these plans were dropped as a result of Project Itoh's death from cancer. Novelizations for these games were eventually written by other authors.
Kojima originally wanted the Beauty and the Beast Unit to be naked during cutscenes. In addition, according to Yoji Shinkawa, the motion capture actors were asked to do the motion capture nude. This was scrapped because it would have affected the game's rating.
Concept art shows two male characters that were cut from the game known as Snake-Man and Adam.
Originally, Johnny's grandfather, also named Johnny, was going to appear at the wedding, confirming that he had survived the events of Metal Gear Solid 3. Unfortunately, this never made it past the concept art stage.
Writer Revolt: Originally, Kojima wanted to end the game with Snake and Otacon turning in to authorities only to be executed for being terrorists, which, given he's wanted to end the series even at this point, could be seen as this in itself. However, his staff had their own revolt towards the idea and flat out refused to work on the game if it was to end that way.