Hey Its That Guyver. Hayter was credited as Sean Barker (his character in Guyver) in the demo version of the game. In released version, this is no longer the case.
Also, in Japan Snake is Anavel Gato, the Nightmare of Solomon.
Dr. Naomi Hunter is, depending on which version of the game you're playing (since her accent changes from MGS original to TTS), either Bastila Shan or Electro Ovilo. Of course, they're bothJennifer Hale, who is also known as Fem!Shepard, Samus Aran, and, well... a lot of other people.
Revolver Ocelot is also known as, believe it or not, Elroy Jetson.
Sniper Wolf (Tasia Valenza) has also been Poison Ivy and Spider-Woman though, really, neither of these is a stretch.
In the original release of the game, Donald Anderson (the DARPA chief) and Gray Fox were the same person - also known as Greg Eagles, who also played Afro's father and Sulik. In the remake, the latter became Rob Paulsen, who was also Anomen and Pinky.
Throw It In: Gray Fox's presence as the Cyborg Ninja, not to mention the entire concept of the Cyborg Ninja, was not originally supposed to be in the game: Yoji Shinkawa suggested that they add in the concept because it seemed cool.
What Could Have Been: Hal Emmerich/Otacon's appearance was supposed to be more indicative of a combination of Dennis Nedry and Michael Moore (IE, an overweight slob with a baseball cap and always eating a chocolate bar). The design used in the final version was pitched in by Yoji Shinkawa as a way to rebel against it.
Decoy Octopus was supposed to have a boss fight, but it was scrapped due to them not being able to do what they wanted with it. Aspects of the fight were used in Metal Gear Solid 4 in the Laughing Octopus fight.