Snatcher/WMG

Gillian Seed is an Alternate Universe version of Solid Snake

 * First, Kojima frequently puts AU versions of his own characters into other games, making this possible, and maybe even likely. We know that Metal Gear TX-55 existed in the Snatcher universe, as displayed by Metal and mentioned by Harry. Pettrovich Madnar (spelt 'Modnar' in the English version of Snatcher to facilitate a Sdrawkcab Name), the Metal Gear developer, was working on the Snatcher Project; and in the Metal Gear universe, Big Boss was brought back after Outer Heaven thanks to the actions of that universe's Snatcher Project. It all starts to add up:
 * The Catastrophe occured on June 6, 1996. After Outer Heaven (1995), Snake joined the CIA - the organisation Gillian was an agent from. Why wouldn't the mission controller send in a spy who has already dealt with Madnar? Madnar did not consensually work on the Metal Gear project - Snake was probably sent in to work with Madnar, being someone Madnar already knew and trusted. (He was using the name 'Gillian Seed' and was disguised - MGS4 is kind enough to observe that the two look alike, with Snake's 'Eastern European' outfit, which has him dress as and style his hair like Gillian.) His marriage of Jamie was likely a cover story. After the Catastrophe, Snake underwent severe brain damage during the stasis, and the reconstructors gave him a more agreeable (but still clearly recognisable) personality, based on what information about him and Jamie they could find.
 * Actually, the Catastrophe occurred in 1991 according to the Japanese version, although the original Metal Gear didn't have any actual date for its setting (1995-6 was only established in Metal Gear 2).
 * "Gillian" was then immediately taken in by the army and given extensive training; being Snake, he was a prodigy. The robot designed to have a perfectly complimentary personality to him acts like Otacon, Snake's soulmate in canon (MGS4 also points this out). Gillian even says 'Metal Gear?!' and 'Outer Heaven!?' more than once or twice - likely memories of his old self. His Japanese voice actor even sounds a lot like Snake's Japanese voice actor, but a little softer (this was pointed out in Metal Gear Solid: Portable Ops, where Gillian's Japanese voice actor played Big Boss's Evil Counterpart).
 * Even the obvious contradictions are addressable. Gillian's age was determined to be in his early thirties when he was removed from the cryogenic chamber, based on 'cellular fission rate'. However, considering Snake's advanced ageing, it would make sense for him to be physically thirty-something in his mid-twenties.
 * There is one other problem - Harry. Gillian fathered a son, but Snake was sterile. The reason why is that the kid was a clone. With the marriage as a cover story, Gillian could freely inseminate Jamie with an embryo sent to him by headquarters. Harry resembles Gillian, and looks nothing like Jamie. He also mentions that he looks older than his actual age as a result of brain-activity increasing, lifespan-shortening drugs given to him as a child. Obviously the drugs were placebo, to hide the advanced ageing and 180 IQ he inherited from the "legendary mercenary".

Katrina is there for Author Appeal.
Most Game Developers Are Dirty Japanese Men, and Katrina was 14 before her Region Relevant Age Up. Do the math. (And before anyone asks about Isabella, we all know Metal Gear is pining for her.)

Gillian Seed is a Snatcher.

 * Or, if he were, it would at least make the game a complete Blade Runner knockoff instead of just a partial one.

Gillian Seed is Slowbeef.
Or rather, Slowbeef is Gillian Seed, having forgotten all traces of his prior existence save the word Snatcher, and forced to repeatedly record himself playing Snatcher on the Internet in an attempt to bring back his memories.