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.
Contested Sequel: Metal Gear Solid: Portable Ops bears the distinction for being the only mainline Metal Gear Solid game not directed by Hideo Kojima himself and has a peculiar position in the series' canon as a result. Initially advertised as the "missing link" between the events of Metal Gear Solid 3 and the original Metal Gear, it essentially tied up all the loose ends between those two games (showing how Big Boss first formed FOXHOUND, met Roy Campbell and Frank Jaeger, and obtained the funds for Outer Heaven) and even foreshadowed the events of Metal Gear Solid 4. But despite the generally positive reception it received during its release, Kojima was unsatisfied with Portable Ops and went on to direct the next PlayStation Portable game in the series, Peace Walker, which he wrote as a direct continuation of Metal Gear Solid 3, ignoring everything that happened in Portable Ops aside from a single reference in which Kazuhira Miller tells Snake that they can finally "leave all the crap in San Hieronymo behind."
Deader Than Disco: You can tell Konami doesn't care about this game when they had several compilations of the series and only once did they include Portable Ops.
Fridge Logic: One of the better ideas in this game is also one of the most flawed. Specifically, the player can capture enemy soldiers and bring them over to their side, and they even retain their old uniforms, letting them pass by soldiers dressed in the same uniform (there's more than one military faction in San Hieronymo). Seems fair, right? Except that this also means there's no allowance for variation at all. A female officer can't fool a male officer, but can fool other females. For that matter, an officer will stick out like a sore thumb to regular balaclava-wearing grunts, and vice versa. This unpolished idea was removed entirely in the game's sequel, Peace Walker.
Fridge Brilliance: Sokolov's survival was explained in the Metal Gear Solid 4 Database by claiming that he took a False Death Pill during his interrogation by Colonel Volgin, which was given to him by The Boss.
The cell where Snake is locked in at the beginning of the game seems ridiculously easy to escape from, especially considering the room next to it just happens to have a CQC Enhancer suit that conveniently fits Snake. It was Campbell, who unscrewed the vent in question, but was unable to actually use the escape method in question due to being relocated to a different cell before he could even get the chance to use it. Cunningham was probably responsible for unscrewing the other vent and leaving the MK22 and CQC Enhancer suit with Snake's size, however.
In the manual for Metal Gear 2, Campbell's bio mentioned that he was, during this time, the only officer to remember the FOXHOUND of the Big Boss days, which made absolutely no sense when the information about FOXHOUND explained that it was formed in the early '90s, which meant that FOXHOUND was around for, at the absolute earliest, nine years. This game explains exactly what the bio meant by that.
Game Breaker: The M870 shotgun is ridiculously effective against half of the bosses (namely Python, Null and Gene).
Jerkass Woobie: Cunningham is pretty much a big jerk and somewhat two-faced towards FOX and the CIA, but considering what he had to put up with (being forced into a desk job after his leg was amputated, not to mention learning that the CIA basically left The Boss to die, which in his views was an insult to the memory of the Mother of Special Forces), it's kinda hard to blame him for what he did.
Recycled Script: Grab Metal Gear Solid. Replace Solid Snake with Naked Snake, Liquid Snake with Gene, FOXHOUND with FOX, Deepthroat with Ghost, and some other changes and you'll get the script of Portable Ops.
Scrappy Mechanic: Whose bright idea was it to have your teammates die permanently in combat? Fortunately, this was remedied to be more tolerable in the sequel.
So Okay, It's Average: At worst, the game is regarded as enjoyable or at least accepted as part of the series, except it delivered far less than was promised.
Villain Sue: Gene. Compelling Voice/Charm Person, beats up a one of the strongest Metal Gear characters in battle and has them as one of their minions, is an evil counterpart to Big Boss like Liquid is to Solid Snake, is a Super Soldier/ultimate battlefield commander, has Super Speed, and created his own upgraded version of CQC. Not even Ocelot or Steven Armstrong were this bad.