Metal Gear REX defeating Metal Gear RAY. By all logic, REX shouldn't even be functional, having had its sensors destroyed, being blown up, and being left exposed to arctic conditions for years. Yet it goes toe-to-toe with RAY, which was explicitly designed to destroy REX units. Not to mention the fact that Solid Snake had never piloted a Metal Gear before, while Liquid Ocelot had spent time in the VR and had been piloting a RAY for years. Few people seem to mind this particular ass pull, though.
Depending on one's opinions, there's a lot of story moments, but one stands out due to how it plays out: Raiden stopping Outer Haven from crushing Snake at Shadow Moses, only for himself to be crushed and seemingly killed. Despite all the posturing of the cutscenes involved that would signify death for pretty much any other character in the franchise, he's back and only missing his arms and put in extreme care afterwards, and even returns to kick ass with brand new lightning powers for the final act. It's almost like Raiden was supposed to die, only for the writers to revise and save him from the brink.
Author's Saving Throw: Two. The main one was Hideo Kojima's attempt to turn the much-ridiculed "magic hand" plotline into something remotely sensible (which more or less worked), but a lesser one was a bone of contention from Metal Gear Solid: it was believed by Metal Gear Solid 2's non-direct mention of Meryl Silverburgh that Snake had cracked under Ocelot's torture, the "Otacon" ending was canon and Meryl was dead, which fans thought hugely out of character for Snake.note Although it should be noted that the in-game book In the Darkness of Shadow Moses: The Unofficial Truth mentioned that Meryl survived the events of Shadow Moses, and the two references to the book in the game itself implies that it was actually the Meryl ending that was canon, as well as the nod to the Infinity Bandana.
Awesome: Video Game Levels: Twin Suns. A nostalgia-laden romp through the ruined Shadow Moses facility, topped with a sequence where you get to pilot Metal Gear REX and have a one-to-one giant robot fight with Liquid in his Metal Gear RAY, makes this a fan favorite.
Base-Breaking Character: Naomi. Some fans like her characterization and Character Development due to how it shows how much she has changed between Metal Gear Solid and Metal Gear Solid 4. Others consider it be contrived due to her being well liked in-universe despite being manipulative, and how she was directly or indirectly responsible for some of the game's biggest plot points.
Shortly before you revisit Shadow Moses, Snake has a dream where he's on Shadow Moses in his youth, and you have to play a brief scene from Metal Gear Solid. Besides earning FaceCamo that makes Snake look like he did in the first game, there's no point to this dream.
When Outer Haven first rises from the ocean, we get a shot of "Mount Snakemore": a reproduction of Mount Rushmore built into Haven's hull, with the likenesses of Big Boss and his clones in place of Washington and company. It appears on-screen for all of three seconds, after which it is never seen or mentioned again.
In the final act, Raiden suddenly appears just in time to save Snake...with the new ability to conduct electricity. He proceeds to take care of the FROGS by electrocuting them. This fit his name well, but how and why it happened are never explained.
The mid-credits epilogue where Big Boss turns out to still be alive. Either it ruined a perfect ending with what was essentially a 20 minute rant filled with retcons, Deus ex Machina and strained metaphors about Zero's name, or it was a beautiful if somewhat flawed resolvement of Snake and Big Boss' relationship.
The story in general. Some fans find that it is a good conclusion. Others think it contradicts everything previous games told (most notably the ending of Metal Gear Solid 2). The changes that bothered fans are Snake's depressive personality even though Snake is already used to these situations (David Hayter came to complain about some of his actions), Meryl's romance is considered an Ass Pull, Raiden going from a normal man happy with his life to a depressed badass cyborg, Sunny overshadowing Otacon and Naomi despite her young age and several plot mysteries being explained away with nanomachines.
The incredibly long cutscenes. Some have no problem with them since the franchise already had pretty long cutscenes in prior games. Others feel that the cutscenes makes the game feel more like a movie due to their length (the ending in particular clocks in at just about an hour).
Contested Sequel: From a fan standpoint, the game is either a fantastic finale to a great franchise, a game that isn't as good as Metal Gear Solid 3 but still entertaining in its own right, or a substandard military shooter with a story that ruined the series. In retrospect, it's often seen as Kojima's Jumping the Shark moment, due to its excessively convoluted story.
Continuity Lock-Out: Anyone jumping right to this game without playing the previous ones will have absolutely no idea what's going on, with the game constantly introducing characters and concepts whose true significance won't be clear at all without prior knowledge of the series, right from the get-go. This is presumably why the Metal Gear Solid 4 Database was released, so that series newcomers could consult the Database to catch up on the previous titles.
Demonic Spiders: Gekkos. There's quite a lot of them in Act 4; chances are if you don't run into a Gekko, you'll get swarmed by Scarabs.
Ear Worm: The tune being whistled by the guy you have to trail in Act 3.
8.8: Combined with Critical Dissonance. The game received spectacular scores; however, a number of reviewers mentioned they would have given Metal Gear Solid 4 a perfect score if not for those long cutscenes. Of course, for most fans who have grown emotionally attached to the characters and followed the storyline throughout the series, long cutscenes aren't necessarily a bad thing. In retrospect, the dissonance now works in reverse; the game has received considerable Hype Backlash in the years following its release and now has a sizable hatedom, in contrast with its positive critical impressions.
Faux Symbolism: EVA hands an apple to ADAM (a.k.a. Ocelot), who crushes it and throws it away.
In the third stage, you're supposed to be disguised as Young Snake and sneak past the guards while tailing your mark. If you switch your FaceCamo to anyone else, though, everyone in the entire level ignores you.
Stay close to the resistance fighter when he's disguised as a PMC soldier. Not only does he ignore you, but the mercs in the area do, too - especially since there's a Humvee in the area that makes rounds every so often. It also depends on whether or not you've got a gun equipped.
When fighting Crying Wolf, hiding under the truck directly in front of Snake as the fight starts will make Snake impossible to damage except from directly in front, give him a fixed 99% camo index, protect him completely from stress or stamina loss due to the blizzard, and make the whole battle a matter of waiting for Wolf to wander into view and blasting her with the biggest, meanest gun at Snake's disposal when she does (unless you already have her rail gun, which is too bulky to use while prone but will pretty consistently kill her in one shot).
A major oversight occurred when prize matches for Automatching first came out in Metal Gear Online. It made automatching much more attractive, with the potential to receive up to 400 reward points (points which you can spend on in-game gear for your character) for winning a deathmatch game. However, in the case of a tie, both teams won the points. Players quickly realized that if everyone agreed to not do anything for the whole five minute match, everyone would get 400 points. Players farmed for thousands of points for a week until the next update, which lowered the amount of points earned to 200 points and awarded nothing for ties.
One gun towers over all others: The M14 EBR. Breaking tradition, not every gun in the game insta-kills with a headshot, but this one still does. It has a very large magazine, uses common ammo, and can be silenced. It also features full-auto as well as single-shots modes, so you can still use it in close combat, with slightly more power than the M4. The scope means that those long-range headshots you used to be so proud of with the pistol in Metal Gear Solid 2 and Metal Gear Solid 3 are now ridiculously easy, so you can pop off a few headshots and immediately remove whatever "sneaking" you might've had to do. The real kicker though? It's a Disc One Nuke. It's so early that you can often buy it immediately after meeting Drebin with the points you earn retroactively from everything before meeting him because it's so damn cheap - or, if you want to save those points for more suppressors, just steal and unlock one from the snipers in the very next map area after meeting Drebin.
Act 4 has at least one area that easily allows you to farm Drebin Points: simply equip as many healing items as you can, let the Dwarf Gekko in the tank hangar spot you, and then let one of them knock you over. They'll begin pulling out guns and shooting at you at this point. The thing is, though, Dwarf Gekko have three hands, but are using two of them just to stand up, so they can't reload - once the mag is empty, they toss the gun away and pull out a new one. Endlessly. Most of them have the GSR, but a few will also drop the Desert Eagle, which is otherwise unobtainable except by buying it from Drebin (thus saving points if you plan to use it later) and worth ten-thousand points afterwards. In about thirty minutes you can make a million points by simply not killing the swarming Dwarf Gekko.
Goddamned Bats: Scarabs. Imagine a tiny, three-armed robot (often holding a gun in one hand) capable of rolling around, hanging onto a wall to act like a security camera, and grabbing onto you to deliver an electric shock. Now imagine dozens of these little bastards climbing all over you because you triggered an alert. For bonus irritation points, they're small enough that it's easy to not notice them the same way you'd notice a tall human, and you could wind up wandering right into their path. Chaff grenades, the one thing that can stun machines in this franchise, are also extremely rare in this game.
The Metal Gear Solid 4 novelization features a lot of reference to religion, the Bible, Christianity, Jesus, and God at various points. Project Itoh certainly at least met them shortly after writing the book.
Snake's comments about Samus Aran in Super Smash Bros. Brawl - namely, that he's attracted to her - become this upon the introduction of the Beauty and Beast Corps; an entire group of women who wear "sneaking suits" and big power armour, just like Samus does. Not only could he not tell that they were women at first (unlike with Samus), but he seems mildly repelled by them. Guess they're not "your kind of woman" after all, eh Snake?
An episode of Transformers titled "Only Human" featured a character heavily implied to be Cobra Commander, of G.I. Joe. As that episode was set in the future, he went by a different name - Old Snake.
Magnificent Bastard: Do you even need to ask? Ocelot was already a Magnificent Bastard in Metal Gear Solid 2 and Metal Gear Solid 3 but with this game, he became one of the most magnificent bastards in all of fiction.
The Patriots' use of a quadruple amputee - namely Big Boss - with nanomachine-induced Locked-In Syndrome as the key to their network. Who is then thrown into a fire when he has served Ocelot's purpose. The fact that it is actually revealed later to be Solidus in the fire does little to ease the creeps.
Laughing Octopus. Everything she does is disturbing as hell. Laughing uncontrollably while killing people is bad enough, but some stuff is just wrong, like imitating Old Snake's face (while still using her own voice) during a session of killing a bunch of prisoners. Her boss fight makes full use of her ability to imitate nearly anything with her octopus-like mimicry, also leading into Paranoia Fuel as you try to hunt her down. The music that accompanies her is also appropriately disturbing.
Vamp's overall appearance is much more unsettling now than when we last saw him; an unhealthy skin color, nasty-looking veins in his face, red eyes, and the scar from the gunshot wound he received to the head in Metal Gear Solid 2 before his healing was nano-enhanced to fix such wounds instantly and without reminders. He's also got dog tags which appears to be his current method of counting kills, although these could be Dead Cell's tags; the number is right if you count Fortune's husband, Chinaman and Old Boy, and we never see him add any more (then again, we never see him directly kill anyone in this game either).
Rosemary. Most fans didn't care for her overly dramatic and annoying moments over the Codec in the second game. In the fourth game, fans didn't like the fact that she was married to Colonel Campbell, although once it was revealed she did it to protect Raiden and their child, fans warmed up to her. Her conversations with Snake about psychology were also very well written, not to mention they weren't forced on the player ever hour or so like in 2.
Scrappy Level: Third Sun doesn't get very much love, thanks to its very high Story-to-Gameplay Ratio, starting out with a long, slow trailing sequence which leads into a series of long, exposition-heavy, retcon-laden cutscenes. Many players felt that the action sequence after said cutscenes, along with the following boss fight, redeemed it a little bit.
Scrappy Mechanic: The game railroads you into using the Operator and much more rarely M4 Custom after certain cutscenes. While they are decent weapons with plentiful ammo, it's pretty jarring if you want to experiment with other pistols and assault rifles; you're forced to limit yourself from five active inventory slots to three while keeping the Operator and M4 in the other two, or to ruin the effect of the cutscene transitioning into gameplay by going into the menu to swap weapons because the game replaced whichever one you actually wanted to use with the Operator.
Shocking Swerve: Liquid never came back from the dead; Ocelot was using a combination of nanomachines and hypnotherapy to make himself think he was Liquid.
Vamp. If you go into the battle without knowing how to properly execute a CQC hold then you can be totally screwed, as failing to execute the hold exactly right at a critical moment of the battle will result in Vamp just knocking you flying, regenerating all his health and continuing the battle. Ditto if you don't realize that the syringe is an equippable combat item.
The battle against Laughing Octopus is also by far the most difficult fight of the Beauty and the Beast Unit.
Crying Wolf is a close second due to the fact that there are very few places you can hide in the arena to lower your stress, making you have to waste ration after noodle after Regain™ to keep your stamina up if you don't know about them. Especially troublesome for emblem runs that don't allow you to use healing items or waste time.
They Changed It, Now It Sucks: Some fans claimed the improved shooting mechanics and the ability to buy limitless amounts of ammo from Drebin at any time turned Metal Gear Solid 4 from stealth game to a third-person shooter with stealth elements. Of course, you can still be shot to pieces easily if you don't watch yourself, even on normal difficulty, so stealth is still required, especially if you're in a heavy combat zone between two different groups, at least one of which will shoot you on sight. There's also the fact that you get less points for dropped weapons if you kill the owner (versus getting full price if you hold them up) and have to spend more to get ammo if you've been killing a lot of people.
B&B Corps: It varies whether you find their backstories woobify them or cross into outright silliness. Drebin's apparent omniscience certainly doesn't help with the latter.
Old Snake: Aging at an accelerated rate thanks to being a clone, Old Snake also has to cope with his growing irrelevance and the fact that he is well on his way to becoming a Person Of Mass Destruction. Actually, the last bit turns out to be false, though he doesn't know this until after the credits have already started rolling. And then there's the microwave hallway.
Otacon: In particular, Naomi seducing him to procure information for Liquid and Vamp. Her betrayal, double betrayal, and subsequent death, really hit Otacon hard. He's also keenly aware of how little time Snake has left to live, something that he's clearly finding difficult to cope with on top of everything else.
Raiden: In addition to all the stuff he had to deal within in the second game, Raiden now has to deal with having been tortured beyond human capacity, turned into a cyborg killing machine (a la Gray Fox), seeing his girlfriend go off and marry the much older Colonel, and coping with the fact that their unborn child died in a miscarriage. Fortunately, the last two turn out to be false, and the first seems to be remedied in the epilogue.
Big Boss: Not dead, but instead induced into an artificial Locked-In state so that he can be used as the key to the world's Evil Overlord computer, one can't help but feel sorry for the guy. Until after the surprise ending, when it turns out it was more likely Solidus Snake that suffered the sad fate of being thrown into a fire.