Victini being the first Pokemon in the Unova Pokédex ties into its theme of victory. Oftentimes, one is victorious when they have achieved the rank of #1.
Let's take a look at Victini. Because of the V on its head, it kinda does look like, well, that one robot with an annoying stage. Let's take a closer look. It has 100 base speed, and also learns 'Quick' Attack and Hyper Beam. Gen. 6 made it even better, introducing Inverse Battles. Now Victini can be weak to 'Flash' Cannon, Celebi's STAB moves, and Excadrill's second typing.
Also, the Greek goddess of victory was named Nike. The American sportswear company Nike's "swoosh" logo kind of looks like an angled V.
Victini's signature move is called V-create, and is obviously referring to both its name and its theme of "victory". However, the name is a little awkward; why not just call the move "victory", or "victorious flames", or something like that. However, the "V" in the little has a double meaning: It's also referring to GENERATION V (5), the generation that Victini is the first Pokémon in. This is even more explicit in the original Japanese, where the move is actually called "V-generate."
The state shell of New York is the scallop. See that thing on Oshawott's chest?
The final form of each of the starters is based on an empire: Serperior is the French empire, Emboar is the Chinese empire, and Samurott is the Japanese empire. Fitting, because New York is the EMPIRE State.
The Gen V common bird was a pigeon. Unova is filled with CITIES! Plus, Pidove adopted a louder cry to be heard over city noise. Darwinian evolution exists in that universe.
Drillbur bears a strong resemblance, particularly in its facial expression, to the Mischievous Mole enemy from Mother 3. The ordinary mole "evolves" into a Chimera, just like in Mother 3!
Throh always travel in packs of five. There are (usually) five people in a Judo team.
All official media has red-striped Basculin and blue-striped Basculin listed separately, even though they are the same species and are functionally identical. The Black version Pokédex entry states that they are very hostile in general and that the red and blue ones start fighting with one another instantly. Add to this that this generation being based on America rather than Japan. They're a subtle reference to the Bloods and the Crips. Basculin is way more likely to be based on Red Oni, Blue Oni. Yeah, they're both violent, but the blue one looks calmer.
Alternatively, being red and blue schools of fish constantly quarreling in a region based of the United States, it’s possible that they also loosely represent the democrat and republican parties, who are well-established to be in constant political arguments and struggles against each other. In rare cases where one can see red or blue Basculin peacefully integrated into and mingling with their counterparts school, then it seems that one side managed to somehow convince and sway the other into joining their school.
Scraggy and its evolution Scrafty are two lizards dressed in a punk-style getup (the latter sporting an additional mohawk and hoodie), and its type is fittingly Dark/Fighting. It was weak to Fighting, one of its own types. Other Fighting types like Machoke and Hitmonlee are based on martial artists with training and some combat strategy, while Scrafty represents an untrained thug. Normally, a trained fighter has an advantage in a fight over someone with no training. Even if two Scrafty fight, it'll be like two gang rivals dueling, since both will use Fighting type moves and go down quickly.
Sigilyph are said to have once guarded an ancient city, which explains what they're doing in the Desert Resort.
At first glance, the Pokémon Trubbish and Garbodor seem to show that the developers have run out of ideas and/or motivation to be creative. However, there's a reason they haven't been in previous generations. While previous regions were based on areas in Japan, Unova is based on New York and the U.S. east coast. Trubbish and Garbodor are actually a reference to the massive landfills and garbage problems that America has.
Black and White is also basically a big reference to the first games. About 150 Pokémon, none from other regions. So, there are some repeating themes. Like the pollution (Grimer and Muk) Pokémon and the trash Pokémon. There's also the new Electric/Flying- and pure Flying-type Pokémon and Pikachu.
In the first generation, we had the Poison-type Pokémon Grimer, Muk, Koffing, and Weezing. Those two families represent toxic sludge and poison gas, or rather, pollution in two states of matter, liquid and gas. Now that we have Trubbish and Garbodor, the trio is complete with the Solid Waste (i.e. garbage) Pokémon.
Despite having a 87.5/12.5 male/female gender ratio, the event Zorua and Zoroark will always be male and female, respectively. Now, consider the genders (and ages) of the illusion people they appear to be at first. This was reflected in the anime by giving them the same genders.
The Vanillite line is one of the most complained about by fans because it's just "sentient ice cream", but what if in the Pokémon universe, ice cream cones were actually inspired by the Vanillite line?
Deerling is found almost entirely in the part of Unova analogous to New Jersey. Anybody who lives in suburban Joisey can tell you how hilariously spot-on this is.
Some people really dislike Klink because it's a strange design. But think about this: Unova is a very technologically advanced region, compared to others. Couldn't it be that they reverse-engineered this from the Pokémon?
And why exactly does Klink's evolutionary line have the least drastic changes with each stage? Consider this: Prof. Juniper stated that Klink appeared in Unova only a hundred years prior to the events in the game. Since Klink naturally existed for only a short period of time, it didn't have the time to make the drastic changes that, say, the Bagon line has made. And note that I said "naturally" for Klink, since the Porygon line (which has made drastic changes in each of its stages of evolution) was created digitally.
Eelektross is stated to live in the water, even though it's a pure Electric-type incapable of learning any offensive Water moves. Water is weak to Electric, meaning Eelektross has a type advantage when it hunts.
Elgyem's Pokédex entry says it first appeared in the desert, so why does it appear in a tower further north? Elgyem is Psychic, and there are two Dark-types native to the area, as well as a couple Bug-types and Ghost-types. So it left the desert and went to live in the Celestial Tower. Makes you wonder why it's living with another Ghost type, though.
Elgyem is more common the further you go up in the tower because it's trying to get the attention of its friends in space.
Their interested in the Celestial Tower can be explained with it being a good place to study certain attributes of human society, considering they're an alien race and all.
Elgyem can learn Ally Switch in Gen V, and Steel Wing in Gen VI onward through TM. Seems a bit random, but what are the TM numbers of those moves? 51.
Cryogonal's name comes not only from "Kryos", Greek for coldness, but also because it's crying.
Golett are golems created by an ancient civilization and are only found in the Dragonspiral Tower. They were probably built to defend Reshiram/Zekrom or, given how destructive their power is said to be, in order to keep them in there. And given how their secondary type is Ground, which is super-effective against Fire and Electric...
The Golett family can't learn any moves from breeding. Statues don't breed.
Of course the New York-based region would have a golem-based Pokémon given its high Jewish population.
When a Pawn (Pawniard) reaches the other side of the chessboard, it may be promoted into a Bishop (Bisharp). Also explains why Ghetsis has a Bisharp.
Generation IX introduced a new evolution that continues the chess theme, Kingambit. Kingambit is described as the head honcho of the Pawniard evolution line, and the king in chess is the "leader" of the pieces, such that being unable to prevent the king's capture (checkmate) causes you to lose. Additionally, Kingambit's idle pose seems to depict it sitting whereas Pawniard and Bisharp are standing. In spite of his importance, the king is also one of the least mobile chess pieces.
Vullaby. The cute baby vulture... who wears a human skull! (Can't find it? Turn the "diaper" upside down.)
Its Pokédex entries somewhat confirm this — Vullaby's protective covering is made of bones gathered by Mandibuzz, which it discards upon evolution. Mandibuzz is based on vultures. Vultures are scavengers. Of course, when tied with the above theory, it would imply that Mandibuzz feed on human and Pokémon corpses and steal their bones...
The reason Mandibuzz and Vullaby decorate themselves with bones isn't just because they happen to have a macabre fashion sense, but also as a readily available food source. Looking at it in a rational perspective, there is no reason why an animal would run around wearing bones for clothes. They don't offer much protection against weather, and for a flying-type Pokémon, they'll just weigh them down while in the air. Additionally, Mandibuzz and Vullaby don't have the kind of limbs or digits that would allow them to wield them like weapons like Cubone and Marowak. Furthermore, since Mandibuzz is listed as an all-female species with no true male counterparts, the possibility that the bird Pokémon use the bones to attract mates is also out of the question. However, while the idea of an animal eating and digesting something so hard and indigestible may seem bizarre, in comes the Lammergeier, a species of old world vulture whose diet consists mainly of bones. In fact, the bearded vulture is one of the few animals on the planet able to subsist on a diet that is 90% bone. That means that whenever the Mandibuzz and Vullaby are hungry, they fly in the air, take the bones adorning their bodies, and drop them off a steep cliff so they can break them open so they are easier to digest.
Some further brilliance regarding Vullaby and Mandibuzz: Dark-types? Check. Vultures? Check. All-female? Check. Vullaby and Mandibuzz are basically supposed to be harpies.
In Gen V there's a new anteater/ant duo. The anteater is a Fire type, and the ant is Bug/Steel, which means the anteater clearly has the upper hand, a very odd thing for a rivalry. Problem is, it isn't supposed to be a rivalry after all.
Deino and Zweilous have the Hustle ability, which raises their attack, but lowers their accuracy. Deino and Zweilous are blind, and they don't get eyes until their final stage!
It ties in with Fridge Horror, but Zweilous has two brains. Hydreigon has three heads, but one brain. The fact it takes the longest of any Pokémon to evolve makes sense; the heads don't want to die/be merged!
Similar to how Gen 1 hid Spanish in the Legendary Birds' names, there is German in one of the Gen 5 pseudo-legendary evolutuion families: dEINo, ZWEIlous, and hyDREIgon. Again, one, two, three.
Why does Zekrom's Fusion Bolt appear as blue lightning? It is meant to show opposition against Reshiram's red Fusion Flare, similar to the Basculin example above.
Kyurem has just got a Zekrom form and a Reshiram form. However, these still have ice on them. This is because it's not complete. Kyurem is the body from which both Zekrom and Reshiram came from. It's not complete without both of them.
In addition, which half of Kyurem thaws/stays frozen are different between the two forms. Black Kyurems left half is still covered in ice while White Kyurems right half is still covered in ice.
Why can Elgyem and Beheeyem learn Steel Wing if they are neither Steel- or Flying-types? Steel Wing is TM51. Elgyem and Beheeyem are based on aliens. And where do people suspect that the US government is hiding and experimenting on aliens? Area 51.
The Animal Stereotype for foxes is to be cunning and deceitful. Zoroark is this weaponized.
Why can Cryogonal learn Attract when, as a genderless Pokémon, it can't use it? Well, whenever it snows in a gentle, picturesque manner, don't the snowflakes just attract your attention?
At first, it would seem strange that Alomomola doesn't evolve from Luvdisc despite their similarities, but the introduction of the Wiglett and Toedscool lines in Pokémon Scarlet and Violet might provide a plausible reason for this. Wiglett, Toedscool, and their evolutions resemble Diglett, Tentacool, and their evolutions, respectively, and were believed to be Paldean variants of them, but they turn out to be completely different species. They just so happen have similar traits to adapt to their environment, which is known in real life as convergent evolution. With this in mind, it's possible that Alomomola just happened to resemble Luvdisc to adapt to Unovan waters, which is why it's not related to it by evolution.
In a way, the Forces of Nature's types are still connected to the elements of The Four Gods that they're based on:
Tornadus, based on the Red Phoenix of Fire, is a Flying-type. Fire needs air (more specifically, oxygen) to burn.
Thundurus, based on the Blue/Green Dragon of Wood, is an Electric-type. Both Electric and Grass are super effective against water. Also, powerplants, anyone?
Landorus, based on the White Tiger of Metal, is a Ground-type. Metal is extracted from the earth.
Finally, Enamorus, based on the Black Turtle of Water, is a Fairy-type. Magic could be seen as flowing like water, not to mention that Fairy is seen as a more "feminine" type and that water is also seen as a feminine element in the east due to its association with yin.
Why do regular Cubchoo and Beartic lack the Thick Fat ability? After all, wouldn't a warm, buoyant, nourishment-storing fatty body be a good thing for polar Pokémon to have, and wouldn't they be plumper than their more temperate relatives? Well, they probably already DO have enough blubber to survive the cold, but their fat is more evenly distributed throughout their bodies and/or this fat can protect them from cold, but not heat (their Ice typing not helping matters against Fire), so it doesn't qualify as the Thick Fat ability, which protects from both Ice AND Fire moves.
According to the Pokédex, Yamask's gold mask is its face from its time as a human before turning into a mummy. Cofagrigus is a coffin ghost that swallows humans whole and turns them into mummies. Now you get to know how they reproduce...
And you can breed them with other species of Pokémon, including Ghost-types. G-ratednecrozoophillia!
Also, you can train them like any other Mon. Yamask clearly remember being human beings, so they're essentially condemned to slavery.
Ghetsis has one. The above make this horror in itself. But there's more to it: given that Ghetsis' Shadow Triad have Undying Loyalty to him, what's to stop Ghetsis from having them entomb his remains so he can become a Cofagrigus himself? Given no-one's managed to catch him even in the sequel, expect your protagonist to be haunted...
Made worse by the fact that the game takes place in Unova, which is said to be like America, where abortion is considered a hot-button topic (right to life vs. pro-choice).
Alternatively, Solosis getting Explosion could be a reference to apoptosis (i.e. programmed cell death), wherein cells break themselves apart in response to a signal telling them to self-terminate. Apoptosis is actually a fairly important process in embryonic development, contributing to the formation of fingers and toes among other things.
Deino starts off with one head, then evolves into Zweilous, who has two heads that hate each other. Zweilous evolves into Hydreigon — who only has one brain and two brainless (and quarreling) heads for hands. Judging by their behaviour, one may end up killing the other. Leaving a single brain. Would it be stunted, or evolve?
What if Hydreigon's main head is a new one? That wouldn't require one of Zweilous's heads to kill the other... But on the other hand, it would mean that the two hand-heads are Zweilous's heads, so it losesboth of its old brains.
And guess what? Ghetsis has one at Lv 54. Which knows Frustration, that move which requires the Pokémon's friendship stat to be the lowest as possible in order to be stronger.
So, what exactly is Deino's evolutionary line like? It has the second-longest evolutionary cycle from egg hatch to first evolution (beaten only by Larvesta), but what is almost definitely the shortest jump between first and second evolution in all psuedo-legendary Pokémon, at 14 levels. Well... Deino did kind of grow a second head. That has to take a while. As to how Zwelious got it so easy? Practice, higher level, and those heads did half the work in losing sentience by arguing.
Golurk. So it's a clay golem powered by a "mysterious energy". Given that it's Ghost-type, that's implied to be some kind of Soul Power, which is already a little spooky. But then you have its Ultra Sun and Moon entries. "Some say that ancient people invented Golurk to serve as a laborer. It follows its master's orders faithfully." and "When the seal on its chest is removed, it rages indiscriminately, turning the whole town around it into a mountain of rubble." This adds the strong implication that Golurk is powered by unwilling soulstrapped inside, denied their eternal rest and forced instead into eternal slavery, and the destruction of the seal used to ensure their obedience allows them to go on a grisly Roaring Rampage of Revenge, demolishing the buildings their masters used them to construct. That "ancient civilization" that created them has a lot to answer for...
. The cute baby vulture... who wears a human skull! (Can't find it? Turn the "diaper" upside down.)
Unfortunate Implications, and multiplies it. Capturing and enslaving a human soul is horrific enough, but what if you captured it from the aforementioned Relic Castle? You just enslaved the tortured soul of a civilian who lost their life in a horrible terrorist attack and made it fight for you! and nobody calls you out for it.