These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Big Lipped Alligator Moment: In The Twin Snakes, during the Psycho Mantis scene when he's forcing your controller to move, he begins laughing. A second later, three photos in the back, which show real people in them (specifically, Hideo Kojima, Ryuhei Kitamura, the game's cutscene director, and Denis Dyack, head of Silicon Knights), come to life and begin laughing in extremely high pitched voices that serves as both frightening and quitehilarious. That's never explained nor mentioned again, though it's not entirely out of the realms of possibility that it's all an illusion created by Mantis.
Broken Aesop: The game explicitly delivers its "don't let yourself be ruled by your genes" message during a nice long shot of Liquid Snake's corpse, who was killed by a "smart" virus that targets people based on their DNA.
Broken Base: The Twin Snakes. Worthy and improved remake or insult to a master piece?
Continuity Lock-Out: Many a player will be confused with the incidents of Outer Heaven and Zanzibar Land if this game's their first. Kojima added dossiers in the main menu to bring newbies up to speed, and Snake's in-game dialog does a good job of expositing without being too obvious, unlike in later games.
Taking into account Snake's physical state by Metal Gear Solid 4: Guns of the Patriots, there's this bit from Campbell just after you reach the helipad, provided you clear the Dock without much hassle:
Campbell: Excellent Snake! Age hasn't slowed you down one bit!
Also, Liquid desired to murder Big Boss in revenge for either allegedly being knowingly given the inferior genes by Big Boss or being told by Big Boss repeatedly that he was inferior, and hated Snake partially for stealing that chance. Liquid Snake's voice actor, Cam Clarke, later voices a character who attempts to avenge his father after discovering that he was murdered by his uncle in Kingdom Hearts II.
Naomi Hunter calling Snake out for smoking and pointing out he could develop cancer becomes this in Metal Gear Solid 4 when it's revealed that Naomi had been diagnosed with terminal cancer.
Genre Turning Point: Before Metal Gear Solid, action games traditionally had nothing more than Excuse Plot. This began changing after the game became a critical and commercial smash hit, with its story particularly being pointed out for praise, and noticeably making the gameplay segments even more intense. For games as a whole, the production values, strong voice acting (at a time where most voice acting in games ranged from mediocre to awful) and gripping story, showed the potential video games had for cinematic storytelling, and brought a possibly permanent shift in the acceptable Gameplay to Story Ratio.
Harsher in Hindsight: After defeating Sniper Wolf, Snake ends up talking with her and then, at her request, shot her in the head to euthanize her. In Metal Gear Solid 3, his father, Naked Snake/Big Boss, does something very similar to The Boss late into the game.
Remember the Yoshi doll in The Twin Snakes, the one that, unlike the Mario doll, doesn't actually do much for you when you shoot it other than having it cry its name? Well, with Snake Eater 3D, the Yoshi doll will have a bit more use this time.
Remember when Gray Fox tells Snake "You haven't aged well"? Becomes extremely true by Metal Gear Solid 4 where the genetic alterations made when he was cloned cause Snake to age so rapidly that he looks like an old man.
When Psycho Mantis reads your memory card in The Twin Snakes, one of the games he can read is Super Smash Bros. Melee. Snake would show up in the third game four years later.
In one of the Mystery stages in VR Missions, Snake picks up and dons a hairpiece to resemble Liquid. He's also a dead ringer for Raiden, or Raikov if you prefer.
It's Easy, So It Sucks: The Twin Snakes included many features originally introduced in Metal Gear Solid 2: Sons of Liberty, but the level design was hardly changed at all to match the new features, leading many players to complain about how much easier the game is when you can aim in first-person view and guards attack in finite amounts - as opposed to the endless waves that would swarm you until you ran out of ammo or died in the PS1 original, not to mention the fact that Snake starts out with full health instead of gaining health incrementally after beating each boss. It's worth noting that the enemy AI in The Twin Snakes is vastly improved over the original, making them much more difficult to run from, hide from, and fight.
The most common criticism of the game, specially at the time. A typical player will finish the game in about 10-11 hours, well over half of which is cutscenes and Codec conversations. This is mitigated by the ranking system, multiple endings, and New Game+ bonus items, but that still smacks of Fake Longevity.
Word of God is this was intentional, as Kojima wanted the game to not take too long to beat for the 17+ age audience that would most likely have a busy schedule and not allow for as much gaming time.
Specifically, it's the fact that the game has two discs that gave people the impression it was going to be longer. Had they managed to squeeze it all onto one disc (which was impossible due to the limits of the technology), this complaint probably would have flown by.
Narm: Just about every cutscene has at least a few moments like this. Repetitive, heavy-handed dialogue with clunky exposition? Check. Villains so over the top and gimmicky with various violent fetishes that have little chance of being taken seriously? Check. Said villains having melodramatic death scenes that stretch on for at least over 5 minutes just to explain their tragic backstoris? Again, check. All topped off with some of the most ridiculously unsubtle and long-winded speeches in a game even by today's standards.
Narm Charm: The over-the-top action scenes in The Twin Snakes go around from being unintentionally hilarious to absurdly awesome. The Twin Snakes may have taken this to the logical extreme, but the original MGS wasn't far behind in this regard.
So Cool It's Awesome: Considered to be a serious contender for one of the best games of the fifth console generation and one of the best stories ever told in a video game at the time. Unless you think...
Seinfeld Is Unfunny: The stealth gameplay may seem rather crude and simplistic compared to later entries in the genre, especially to players who have only played the likes of Hitman or Splinter Cell. The story, which was highly praised at the time, nowadays is considered by the standards of modern gamers as an Info Dump train wreck with way too much Parrot Exposition; though it can still hold up as part of the overarching mythology of the series.
The Psycho Mantis fight was ground breaking and full of HSQ at the time, but most new players nowadays don't get what was so mind blowing.
Special Effects Failure: The graphics in the PS1 original looked... not very good even for the console's standards. Choppy movements, models having jagged textures, no distinguishable eyes, and everyone having the same badly pixelated faces. This is likely to blame on the game originally being slated for the 3DO, with the cutscenes roughly completed in it's engine before development switched to the PS. It's not too far of a stretch to say that the game wouldn't have much emotional depth if not for the genuinely good voice acting holding the story together.
Tastes Like Diabetes: The good ending with Meryl has almost nothing but cringe-induceingly sappy lines about how she and Snake are glad to be alive with each other. Blech.
That One Boss: Sniper Wolf, since the sniper rifle is so annoying to control. Though the second battle can be easy if you use the Nikita.
Most of the criticism of The Twin Snakes come from this. Specifically, it's the over the top Cutscene Power to the Max, the unbalanced mechanics from Metal Gear Solid 2 and the new soundtrack.
Same applies to the redone voice acting. A major point of contention were the removal of Mei Ling's Chinese accent and Naomi's British accent, which fans of the PS1 original thought made them really stand out and either sound cuter (Mei Ling) or sexier (Naomi). Retconning the accents was intentional though as the characters' backstories made their original accents nonsensical (as the former was born in America, while the latter was raised in America since her childhood). When Metal Gear Solid 4 later made the American accents canon, PS1 purists either blamed the remake for "ruining" Mei Ling and Naomi, or just went ahead and reluctantly accepted the new canon accents.
The Untwist: Liquid's identity, and to a lesser extent, he and Snake being twins, isn't hard to figure out hours before the characters do, considering Liquid doesn't really bother to change his appearance or voice in any way, and he's conveniently there to give Snake advice just as Liquid's presumed escaped or dead.
Villain Sue: Simply put, Liquid survives, time after time things he damn well shouldn't. Getting shot up 3 times with military-grade rounds at point blank, his copter getting shot down, presumably destroyed along with Metal Gear Rex, somehow escaping the island after it was being nuked with no explanation, and having a final chase at the very end, exchanging bullets and ramming into each others vehicles, presumably expiring after the injected virus that's engineered to kill him from his specific dna pattern finally gets to him. And not even then.
The Woobie: Poor Otacon got tricked into programming a nuke-toting weapon. He thought that he was working on a nuclear deterrent. He's also pretty awkward and pathetic in this game, which only serves to make the player feel more sorry for him.
Woolseyism: Most of the script was modified during the localization into the English version:
Mei Ling originally quoted only Chinese proverbs in the Japanese version. She would say the original proverb in phonetic Chinese and then repeat the same proverb in Japanese. This proved to be rather difficult to localize, since she simply ended up saying the same thing twice in English, so Jeremy Blaustein expanded Mei Ling's expertise to include Western literature and proverbs as well (this is one of the few changes retained in the remake The Twin Snakes).
Similarly, before dying, Psycho Mantis's line about it being the first time he ever used his power to help someone "[felt] kind of nice" was the result of the original line, "It feels so... nostalgic", (originally a reference to his mom dying from childbirth, an event he at least recalls the emotions of).
Ocelot's line about making bullets go wherever he makes them was not in the Japanese script. It's totally in-character, though.
Snake's explanation about how Liquid would be "chopped up faster than an onion in an infomercial" had he ejected from the Hind was not in the Japanese script. The Japanese script, as well as the rewritten English script for the GC version, was more technical in nature, simply stating that Liquid would be chopped up by the rotor blades.
In the Japanese version, Dr. Clark's gender was alluded to only once, when Naomi responds that it was Gray Fox who killed Dr. Clark (she uses 彼 "kare", a masculine pronoun). The English version added in more references to Dr. Clark being a male. Dr. Clark's gender was retconned in later games.
Liquid's reference to Big Boss always telling him that he was always a failure as his reason for hating Big Boss was not in the Japanese version. The original script, as well as that of The Twin Snakes, simply had him exclaiming outrage that Big Boss seemingly chose him, knowingly, to be the inferior one.
Liquid's mention about Big Boss being in a coma, when explaining the history of the Les Enfants Terribles project, was also a Woolseyism. Originally, he simply stated that Big Boss was sterile. Like Mei Ling's use of Western quotes, this was retained in The Twin Snakes.