With my updated understanding of typology...

I'm going to start typing Metal Gear Solid Novel characters!!! Well, it's just very interesting to me...

Solid Snake: INTJ
Reason: I was torn between ISTP/INTJ, due to his apparently superior use of Se - quick to form judgments on what to do, quickly picks up hints and clues in the current context, and he considers his options within himself - very huge clue of the Ni/Se combo. He has utter lack of Si, and completely no signs of Fe - does not understand conversational roles, and ends up pissing off characters for "rejecting" conversation roles - classic way of pissing people off for non Fe-users, or even SJs who don't know him well enough. His emotions are very contained and he has no wish to be understood (strong signs of Fi). Also has a lack of Ti - has a tendency to draw information from his environment and organize them effective enough for action output, but seldom analyzes things for the sake of it, and discards principles and rules that make no sense.
Conclusion: No Ti/Fe, or Si/Ne. Has a strong introverted inclination. Not an F. By deduction, he's an INTJ.

Meryl Silverburgh: INFJ
Reason: Very clearly an Fe-user - classic clashes of Fe/Ti vs Te/Fi with Solid Snake. Has a strong urge to understand "why", and does not have a very strong attachment to the past - telling of a lack of Si. Like Snake, she has a tendency to work within context. Surpasses Snake in the department of analysis, but has a poorer judgment of what is necessary for the objective goal. Very competent on her own terms and engrossed in her own vision. She and Snake understand each other and are on the same page, but often come to different conclusions. After categorizing Snake as "on her side", she finds herself more easily agreeable with Snake - signs of Fe.
Conclusion: She could be an ENFJ, but has a comfortable use of Ti, indicating a tertiary position versus inferior position.

Roy Campbell: ISTJ/XXTJ
Reason: Actually, I don't know. He has Te/Fi preferences. It's hard to tell if he is an S/N or I/E. Considering his reserved nature, he seems to have introverted inclinations, and prefers to go slow and steady in his speech. His concerns are far more direct than Snake's, and he seems to use quite a bit of Si. Seems to have difficulty adjusting and jumping onto a situation as fast as Snake does.
Conclusion: By deduction again, he's an ISTJ.

Naomi Hunter: ISFP
Reason: Her motivations and reasons are very straightforward, and are actually rationalized, far more than Snake's. She does not relive past experiences - she carries her interpretations (Ni) of events with her and carries on to act on it. It's expected that an Fi-dom learns to control Fi-reflexes in a military background, but it's evident that her emotions catch up with her instantly as she observes Snake throughout the mission. She sees eye-to-eye with Snake, a common thing for Se/Ni and Ni/Se interacting parties, and that both have Te/Fi and Fi/Te makes the connection much easier, and Snake feels this profound connection; they get what each other is saying. She also sheds her past quickly and takes on a new conclusion after she understood things differently.
Conclusion: Her goals are straightforward and easy to understand, as is the case for most Se-Doms and -auxiliaries, versus Ni-Doms and -auxiliaries. No signs of Si/Ne. Her introversion shows very clearly.

Otacon: INTP
Reason: I had thought him to be an INFP, but the Ti preferences started to show later in the novel. He has a strong use of Ne/Si. At the back, he starts to show no signs of Fi at all - he uses Ti reasoning to determine the truth or falseness in a situation, and it even shows in the way he analyses his feelings for Sniper Wolf. At this juncture, he seeks Snake's second opinion, and Snake's Te/Fi reasoning about his feelings for Sniper Wolf confuses him. In MGS2, his relationship with E.E is also confused, and he tries to reason his way out, only to get even more confused. Strong Ti-Ne leads him to have less concerns about consequences.
Conclusion: His emotionally expressive demeanor was confusing at first, but eventually, the Ti reasoning gave way to a huge hint of his type. A rather unusual INTP.

Gray Fox: ISTP
Reason: Very hard to type. I suspect that he gets along with Naomi and Snake primarily because of the Se/Ni combination, and he shows very strong Se use. The Ti process in an ISTP is often difficult to see, but it shows in the manner in which they make decisions and carry out actions. He and Snake's interaction is unique, in that they both know they see the same things, but have a subtly different approach and conclusion. Not a complicated man, but definitely determined.
Conclusion: I might be off the track. Too little to work with, and the fact that he has a damaged persona makes it even harder; he could be ESTP.

Liquid Snake: ENTP
Reason: I don't know why people type him as an XNTJ - no signs of Ni/Se at all. Very outer world focused. He cooks up ideas on the fly, and uses a lot of Ti to back it up. Fe-tertiary in ENTPs tend to show in forms of reaction-monitoring and teasing - evident in his treatment to Solid Snake. A telling sign was when he assumed the existence of a vaccine to FoxDie - Snake questioned Liquid if there truly was a vaccine, but he merely said, "There has to be!" His motivations are also explained in a logical discourse; he mocked Naomi for her silly motivation for revenge, but when Snake pointed out the irony in his own motivation resembling Naomi's, he failed to address it and instead turned it against Snake ("Unlike you!"). His horrible assessment of combat actions to be taken during his control of Metal Gear REX is, to me, a strong indication of a total lack of Se.
Conclusion: I put his functions together, and then compared him to the three ENTPs I've ever known - they sound just like him: grand preachers of their whacked ideas. Entertaining, intelligent...but still whacked.

Sniper Wolf: ISTP
Reason: Her interaction style with Snake is curiously similar to what it is like between Gray Fox and Snake. She has an obvious preference for Ti. Also very adaptive to her current circumstance, indicating use of Se. Her devotion to her ideals tells a Ti-Dom. She and Otacon probably understand each other from the Ti/Fe perspective, but have different conclusions because of the Se/Ni and Ne/Si divide.
Conclusion: Could be completely off the track, since there's too little to go on with. But I can't see her as an Si or a Te user.

Decoy Octopus: The famous XXXX type
Reason: The seventeenth type, because we get to see him only in his afterlife.
Conclusion: I wrote this for fun.

Vulcan Raven: Some...Si-user (XSXJ)
Reason: He is...just weird... Too weird to type. He uses a crap load of Si. He talks too much and he's...I don't know...just weird. He seems absolutely terrible at contingencies, so it's hard to tell if he uses Te/Ti. Seems to be somewhat out of it a lot. He seems a bit like an ISFJ to me, but I really don't know.
Conclusion: The Shaman who can't stop talking about his culture. Has his roots in a very concrete manner, so I doubt that he's an N.

Psycho Mantis: INTP
Reason: I thought about this for a while. His personal ideals are unemotional in nature despite the emotional roots. Has a stronger use of Si compared to Liquid, and his ideals via Ti are of utmost importance. Lack of Se. For some totally random reason, he just had to torment Snake with hallucinations and delusions, a period in which he could simply just whack life out of Snake - seems like a whacked Fe projection or something...or just Ne on the loose.
Conclusion: He has very little consideration for consequences, and simply follows his reasoning. Everything that's happening around him is of little relevance to him - something xNTPs share in common, but often unintentionally.

Revolver Ocelot: ISFJ
Reason: This one was interesting to type. On first glance, it's easy to think of him as an NT, but on further observation of his general conduct, he's a heavy Si and Ti user, and definitely has Fe. The fight between him and Snake in the room with Baker is very interesting, in that Ocelot kept talking about history, and has a tendency to explain his preferences in Ti style - he complained of Snake's SOCOM ("Hah! Everybody uses SOCOM..."), went on to talk about his SAA (despite the disadvantage of slow reload time), and used Ti to figure out how to use the SAA best suited to himself - oddly a behavior reminiscent of Meryl (INFJ: Ti-tertiary), who also explained to Snake her preference for the Desert Eagle and how she had learnt to suit it to herself. He seems to find Snake irritating to talk to, in once again, typical Te/Fi and Fe/Ti conflict. I suspect that Snake has no clue why Ocelot is talking so much to him.
Conclusion: His cognitive functions are the same as INTP, and I had considered him an INTP, but he's a lot more concrete and less flexible in his approach to changes. Interesting, he sees eye-to-eye with Liquid, who shares the same function.

That...was very satisfying to type. What a strangely good way to improve my mood.