If there's one thing every police force in the games show, it's that they're Dirty Cops who hate their job. Sometimes it even crosses into borderline criminal behavior and a love of excessive force, which is clearly shown with the Shen Long police chief in Path of the Furon. Averted, however, by the Albion and Takoshima cops - they have their eccentricities and occasional moments of gameplay-mandated excessive force, but they seem largely free of any brutal or corrupt tendencies.
The Takoshima Defense Force in the second game makes heavy mockery of the Imperial Japanese army, to the point where they remind you that yes, Japan still has an in-name army. Hell, they even outright claim they're attacking the Arkvoodle Cult with violent repression.
The hippies in Bay City are depicted as pot-smoking, self-righteous liberals who attempt to disdain from the "bourgeois" influence of the city, yet are ironically thisthemselves. The Albion hippies are more of a downplayed example, although they are shown as fashion-absorbed, virtuoso rich kids and part-time call girls.
The "squares" in both cities, however, also receive a fair amount of mocking - for being overly judgemental and illiberal on one end to being repressed and in self-denial about their own desires on the other. Bay City's fathers and businessmen are an extreme example. Scan them, and they may display a racist or war-hungry disposition on the one hand, or a rather dark and addictive personality on the other.
Conspiracy theorists. If the first game is anything to prove by, they're either over-paranoid rednecks who think everyone is there to conspire against them, vapid Nerds who are desperate to get ahead in life yet don't seem to realize their obsessions lead them away from women or blue-collar jobs, or homeless protesters.
The game makes heavy mockery of communists and conservatives - Communists being seen as humorous, dim, vodka-drinking men with a heavy dislike of the "decadent capitalists" who live in the USA, yet secretly hate their government, while conservatives are depicted as overly paranoiac Stepford Smilers with a fear of everything foreign due to a Red Scare. These make up a major part of the plotline for the first game, and then a minor fraction of the second game, with the revelation that the Soviet Union was formed by an alien race who intruded Russia during the late 1900s and kickstarted the October Revolution.
Compared to the latter three, democrats are a downplayed example, as they're usually only referenced by quotes said by pedestrians. Bay City's hippie pedestrians in the second game count, as described above.
The UK version of the Labour Party, the Conservative Party, and Margaret Thatcher (whom is called a "hooker" by one pedestrian, and a "middle aged matron with terrifying hair" by another) get this treatment in Albion.
Albion Man: Who can take the Labour Party seriously? Come on, they even have "labour" right there in their name!
Emperor Meningitis appears to be a thinly-veiled mockery of Richard Nixon, sharing his "if the president does it, it is legal" quote upon encountering.
Alternative Character Interpretation: Did Crypto ever really care about Natalya, or was his fondness for her purely sexual? Some of their interactions suggest the former, while the ending, her phone call in Big Willy Unleashed!, and casually brushing her death off in the next game suggests the latter.
Anticlimax Boss: An irritating number of examples, though some are more because you can become rather overpowered over the course of the game (Meteor Gun, anyone?)
Oranchov's Blisk mutant form might give you some trouble, since it comes early in the game. Unless you use the Anal Probe (which you find mere moments before the fight) to turn him human again. He's about as squishy as any KGB Agent.
Played horribly straight in Path of the Furon, in which some of the bosses barely even move, and especially if you have an upgraded Ion Detonator, except for Henri Crousteau.
Base-Breaking Character: Natalya Ivavona. Whether or not she was a decent female companion for Crypto or a mere Reluctant Fanservice Girl made for pure lust for Crypto is of large debate to many people. It doesn't help that many people think that she is often blamed for the Romantic Plot Tumor of the second game, despite Crypto mostly being responsible for hitting on her.
Best Boss Ever: The well remembered fight with Kojira. You're an alien invader fighting a Godzilla Expy across the streets of Not!Tokyo; need we say more?
Breather Level: Most of the Ruin Lives missions are this. They usually follow simple objectives and don't involve killing off or defending a character from enemies.
Captain Obvious Reveal: Silhouette, the Big Bad of the first game, being a woman. There were a lot of hints, and if you read the thoughts of the Majestic agents, they blatantly state it and then try to cover it up:
Majestic Agent: Why does Silhouette give me these jobs? Was it because I hit on her at the Christmas party...? Oh, wait, no one's supposed to know Silhouette's a chick. Scratch that thought.
Cargo Ship: One of the "Ruin Lives" missions in the second game involves destroying a Takoshimese businessman's beloved "New Car-san".
One pedestrian in Albion's scan thoughts is "My mind says BBC 1, but my body says Channel 4" when scanned. While Channel 4 is a real life channel in the United Kingdom, it only started broadcasting in 1982, 13 years after 1969 (the second game's setting).
There are several references to Emperor Hirohito being in control of Japan in the second game, despite the fact Japan became a democratic country after World War II. Takoshima's defense force also acts like a major army, despite the fact that Japan prevents its defense forces from becoming full military units.
The Majestic Agents in the first game. They can rip through your Holobob disguise, giving you away in the most unfortunate of times, and their powerful assault rifles can kill Crypto in seconds if he's not careful. Even worse are the psychokinetic mutants, which can drain down your concentration and render Crypto's PK or Hypnotize abilities useless. They wouldn't be so much of a problem if they weren't the most common enemy you find in the last three areas of the games...
Tanks. Not only can they shoot you out of the air if you're careless, they'll even do it on-foot. Not to mention how they follow the player almost everywhere, making trying to disguise a chore.
Designated Hero: Subverted with Crypto and Orthopox. While they are not pleasant people and are responsible for committing several acts of murder (including the President of the United States), their invasion of Earth is done to save their species from extinction rather than destruction, and they don't advocate for destroying Earth completely as this would remove all traces of Furon DNA. The second game expands on this by having Crypto be disgusted by the Blisks' plan to water-lodge Earth for themselves and start becoming accustomed to human culture, even admitting he doesn't hate all humans. In addition, a lot of Crypto's enemies turn out to be Not So Different (Majestic want total world domination while using the Furons' technology to do so, while the Blisk want to literally destroy all humans), which justifies his invasion somewhat.
SAM missile launchers in the first and second game. In the first game, they launch a single missile that is difficult to dodge and does a crap ton of damage to your saucer. Not to mention, they spawn in the worst of times during already difficult to begin with missions, such as during "It's a Wonderful Armageddon". The damage is toned down in the second game, and the tracking is made less potent, but now they launch THREE missiles at once, and they're now mobile. Add to the fact that on high alert levels, they show up everywhere and can now move, and you will be swooping, ducking, weaving and dodging to avoid the buggers, as they will fill the sky VERY quickly. And to top it all off, there is a graphical bug on the PS2 version of the second game, which removes the exhaust contrail on occasion, meaning you won't see the rockets until it's too late.
The soldiers in the first game can easily become this. Their rifles aren't as strong as the shotguns used by the police force and anything Majestic agents use, but a single shot can still cause a lot of damage to Crypto, they soak up more damage than most human enemies, and they're deployed in groups. What makes it worse is the fact that Capitol City replaces the police force with army soldiers and Majestic agents, making it near impossible to harvest DNA within the city.
Harsher in Hindsight: The secret commentary of the first game found in the second game feature both Crypto and Pox talking very fondly of the possibilities of a third game. This becomes rather harsh considering how disastrous Path of the Furon was.
Crypto constantly getting accused of being a commie and martian in the first game was funny enough, but then the second game reveals that the Bolshevik party did indeed consist of martians in this world.
The Blisk Master Plan for the planet was to water-lodge Earth to make it their haven, since Mars became a barren wasteland during the Martian War. Come 2015, and it has been confirmed that there is actually water on Mars.
The hippies in Albion Crypto can come across are voiced by Robin Atkin Downes, which becomes funnier with the fact that Downes later did one of the voice options for The Boss in Saints Row IV, a game which involves taking down an alien race.
It's Easy, So It Sucks!: Part of the reason Big Willy Unleashed and Path of the Furon failed was due to their lack of difficulty and the buff of several weapons in the game, making DNA collecting very easy.
It's Short, So It Sucks!: All of the games are relatively short. The first two would have been even better if they were longer.
It's Popular, Now It Sucks!: The series has gained a cult following, as well as fan haters, trolls, and the like. Doesn't help that the series took a dip in quality once other developers took over and tried to branch the franchise out with two games at once.
The sounds pedestrians make when dancing will get stuck in your head pretty quick, especially since it's one of the only ways to clear or distract enemies in the area.
"I'M LOSING FOCUS...!" The first game makes sure you'll hear this every time Crypto's concentration meter goes down. This was re-used in the second game for when Crypto loses health, but it does not play as frequently.
Anything the Blisks or Nexosporidium Warriors say.
It says something that the scariest parts of the series are it's main protagonists. Take Crypto himself; a nigh unstoppable killing machine who is able to rip out the brain-stems of humans, destroy entire towns and cities, and even manages to wipe out an entire government agency and alien race. Not to mention, he manages to become President of the United States in the end of the first game. If not for the game's over the top tone, he'd be fucking terrifying.
His weapons can count too - He's able to anal probe people into ripping their brains out and has a Disintegrator Ray as one of his main arsenal. By Path of the Furon, Crypto can summon underground monsters to eat unsuspecting people, cause a meteor shower to land, pause time, summon black holes with a pistol, and even cause a tornado with his saucer. Way more terrifying than it sounds epic.
Oh boy, the Blisk, who are The Man Behind the Man (the KGB) in the second game responsible for attempting to mutate people into aliens and building a superweapon intended to turn Earth into a waterlogged homeland for the martians themselves. Having been driven off Mars by the Furons many years ago, a few refugees crash-landed with their warship in Tunguska during 1908, which had believed for many years to be a meteor crash. Soon after, they managed to kickstart the 1918 communist revolution and took complete control of the USSR. It becomes worse when the Big Bad, Milenkov, tells you that every Premier before him (namely Vladimir Lenin, Joseph Stalin and Nikita Khrushchev) and Leon Trotsky were all leading Blisk members. They make Crypto look like a saint in comparison.
Tunguska, the fourth region of the game where most of the plotline pieces together, is creepy in itself. The area is constantly dark and devoid of anything but green smog, with Red Army soldiers and KGB agents constantly walking the streets and shooting dead possible trespassers to their own base, and the gunfights between Blisk Mutants and security members on the streets. Not to mention how grimly fitting the music and the wolf howls in the area sounds.
The fate of Sergei - After Milenkov captures Natalya off-screen, he mentions infecting him with spores, and that's the last we ever hear of him. Even after Crypto saves Natalya, neither of them bother to save him (then again, Milenkov mentions that trying to cure him wouldn't work), so he's left there to suffer from agony as most Blisk Mutants do.
Only the Creator Does It Right: Pandemic Studios did the first two games in the series, which were well-recived. Locomotive Games did Big Willy Unleashed, while Sandblast Games did Path of the Furon, and as the Sequelitis entry below can attest to, neither developer have managed to live up to Pandemic's initial entries.
The Nexos from Path of the Furon to the Blisk. They look similar and even have a similar reveal (complete with Oh, Crap! moment from Pox), but don't nearly leave the same impact.
Veronica Stone from the same game also counts. She is often viewed by the fandom as just being filler to replace Natalya, and unlike Natalya at least actually helping Crypto in the game, Veronica is merely there to get new things to broadcast and for eye-candy.
Romantic Plot Tumor: Natalya and Crypto. Natalya even gets some status as The Scrappy, despite the fact that Crypto is the one hitting on her. As mentioned elsewhere under Pretend Prejudice, by the time Destroy All Humans! 2 rolls around, Crypto seems to have a desire to make out with anything female. This is worsened by Natalya, as Crypto falls madly in love with her. And so, as a result, Crypto spends almost the entirety of the first half of the game trying to have sex with Natalya, not even caring about what his enemies are up to during the first half.
The Scrappy: Natalya is viewed by some as this, as mentioned under Romantic Plot Tumor, despite the fact that Crypto is the one hitting on her. Natalya even rejects Crypto's proposals and pick-up lines during most of the games. Not to mention how she ends up being Put on a Bus and then dying off-screen in the later two games.
Crypto's jetpack in the first game. What seems like a useful feature (Crypto's only way to travel distances and to reach platforms) is left underwhelming by the fact that it only lasts for around three seconds before the battery level drops, causing the jetpack to sutter. This can cause Crypto to lose health if he lands on a high structure without button mashing, and in several situations it is difficult to maneuver due to sentry guns, EMP mines and S-A-M launchers. Even worse is the fact that it cannot be upgraded. Thankfully, the jetpack does not have a charge level in the next games and is able to be upgraded.
The fact you cannot use weapons at all in a body-snatched form is rather disappointing. On the bright side, however, it makes PK a little easier to use.
Non-mission obtained Furotech Cells in the second game. Most of them are scattered either in easy rooftop locations in a group clutter, or either in extremely difficult locations (e.g. on top of an arch in Albion). Even worse, if you destroy a building in one city, that renders a cell unable to be obtained unless you leave the area, sometimes even permanently unobtainable (e.g. after destroying the Soviet Embassy during one of the final Albion side missions).
That One Level: A lot of missions can end up in this state, especially if Crypto doesn't have essential upgrades or Gene Blends.
In the first game, The Lone Gunman can be extremely tedious due to the swarms of Majestic agents and power-suit mech machines you have to fight off, all while reaching President Huffman's booth. Not to mention how you'll likely need the final Psychokinesis for an extended Holobob capacity, as well as bypassing the Majestic agents who can see past your disguise.
"I Left My Parts in San Fran.. Er, Bay City", a side mission unlocked extremely early in the game, is known for being extremely difficult. The goal is to defend Coit Tower in your saucer against military tanks while Pox tries contacting a Furon general. However, the game spawns an infinite number of tanks until Pox has finished the call, and due to splash damage, it is fairly easy to end up damaging Coit Tower.
Natalya's escort missions are generally amongst the most loathed missions in the game for their tediousness. However, "From Russia With Guns" is, hands down, regarded as one of the worst escort missions in the game. What doesn't sound like such a chore in theory (get Natalya to Soho while killing KGB agents trying to stop her) actually is one. While Natalya is a decent shooter, you have to make sure to not stop a few centimeters away from her or else she will not follow Crypto. It doesn't go without mentioning that Crypto is a no-show for the Elite Mooks, who have machine guns and EMP mines of all things to try gun him and Natalya down. Does it go without mentioning that once you reach Soho, you have to go all the way to Canal Side, despite the fact that from where Crypto and Natalya, Canal Side was just north of where they were? And if it makes it any better, the Saucer part where you have to escort Natalya's car to Canal Side while avoiding freaking tanks of all things is one big joke. And your reward for all that stress? A measly seven Furotech Cells and the Meteor Gun, thankfully.
The Kojira Kaiju boss battle.
The first Arkvoodle Cult mission in Takoshima has the player have to defend the tents from being destroyed by armed forces in the city. What seems to be easy enough (this mission has the same premises as the one in Bay City) is actually even harder, due to a glitch in the game where the timer disappears and is set to 10 minutes, giving you a tedious run-through, and the fact you're dealing with five enemies rather than two (the police, the military, the Yakuza, ninjas, and the KGB).
Made even more so by the fact that when seeing this, he asks how such "intelligent creatures" could do something so disgusting. Keep in mind up to this point in the game, he's referred to humans as filthy or stupid hairless monkeys. This isn't Crypto being his usual rude and aggressive self. This is what he genuinely thought of humanity before witnessing that.
One "Ruins Lives" mission in Albion involves Eddie, a man Crypto meets, who has heard of his wife's friend getting a sex change, but tells Crypto to go away after he doesn't understand him. After reading his mind, Crypto finds out he is secretly interested in getting a sex change himself (although he does love his wife). When Crypto body-snatches him, he calls his wife on the phone, who seems to be appalled at Eddie for wanting this, and then meets him at home. The newspaper at the end of the mission reveals Eddie got the sex change, only to discover his wife left him in the end.
Kojira can become extremely frustrating to beat at first. This is due to her ability to demolish buildings to regain health coupled with the fact that her upper body is nearly impervious to Crypto's attacks. Not to mention her attacks can wipe out Crypto's health bars very quickly.
Crusteau in Path of the Furon. He can empty Crypto's maximally-upgraded health bar in exactly two hits, and whittling down his health bar with the few weapons you have that can hurt him takes forever.
"The Great Cow Race" from the first game. What sounds like an easy mission that one could breeze through in under a minute ("just beat the cows to the finish line; it should be easy using your jetpack") turns out to be a strong contender for the most frustrating mission in the entire game. Aside from the fact that the game's jetpack is notoriously terrible and unable to be upgraded, there's also the fact that the mission causes tons of anti-air turrets to spawn, which means that using your jetpack at all during the mission guarantees that you'll quickly have to endure a hailstorm of bullets that can turn you into alien mince meat unless you get back to the ground and stay there. The mission is damn near impossible to do without enabling the "Bulletproof Crypto" and "Ammo-A-Plenty" cheat codes.
Finding all the probes in the first game. Made worse by the fact that the game gives absolutely no hints whatsoever for finding them.
They Changed It, Now It Sucks: Many people claim that the changes in Big Willy Unleashed and Path of the Furon made them suck, and that they weren't nearly as good as the first two. This is also mostly blamed on the two developers who picked up the series after Pandemic was bought out by EA.
Due to the limitations of the games prior to moving to a next-gen console, the first two games suffer from characters faces not changing outside of cutscenes. It can be a bit unnerving to see someone's corpse smiling or staring into oblivion...
Big Willy Unleashed only made matters worse - Most character's mouths don't move at all and remain expressionless. The Corncob King is one example.
Woolseyism: The Japanese dub, somewhat, in terms of humor: Since most of the humor of the game is based mainly on American cliches of the sci-fi genre, especially from the Alien Invasion genre, and most of the jokes are very obscure for non-American players, the Japanese version went to almost the Gag Dub territory. While the plot is still the same, the characterizations of almost everyone are somewhat different from the original English version. This is more notable with Crypto, since while in the English version he had a deep voice, in the Japanese dub he sounds like Bugs Bunny mixed with a Japanese Delinquent. This is even more hilarious if you take into account Crypto is in fact voiced the same voice actor who officially dubs Bugs in Japan. You can see a clip of that dub here at 4:28.