Piplup and its evolutions are based off of penguins, which are known to live in Antarctica. However, they are able to thrive in other climates. It makes much more sense if you acknowledge the existence of other penguin species that live in South America, Australia, New Zealand, and even Africa.
A major theme in the Sinnoh games is mythology and legends, and this is reflected in the starters: Torterra is the World Turtle, Infernape is Hanuman/Sun Wukong, and Empoleon is Poseidon/Neptune.
Burmy/Wormadam-Trash using urban debris to build their cloaks sounds rather odd, but there actually is a real-life moth larva that does this called the Plaster Bagworm (which isn't actually a bagworm). Although, the debris that plaster bagworms use isn't made of metal, but spiderwebs, fabric, lint, and even hair.
Have you noticed Drifloon/Drifblim's stats? Insane amounts of HP (150 is more than any other Flying or non-legendary Ghost has ever had) but its defenses are quite pitiful. Balloon. It bursts like a balloon!
This is also the reason why Drifblim has the ability Aftermath, which is basically Self-Destruct that activates upon fainting. It is based off of a blimp, and if anyone knows anything about the Hindenburg, well...
The design and moveset of Lopunny make a ton more sense when you think about the species in a survival sense.
Females benefit from their human-like form from being in the Human-Like Egg Group, as it would make sense that male Pokémon with anatomies and mentalities so similar to humans would be more likely to mate with a Pokémon that appears to have the anatomy of a human female, thus leading to a large population of Buneary and a continuation of the species.
Despite the feminine figure, a male Lopunny would likely be seen as a good mate to many Pokémon as well, as the Lopunny species carries many, many egg moves. If breeding with a Lopunny means that the offspring might have an edge in survival against other predators and competitors, it's likely that many wild Pokémon would jump at the opportunity.
Giratina:
At first glance, it seems to be a nonsensical Pokémon that seemed to be thrown into what seemed to be a carefully crafted mythology. All of the other Pokémon Arceus created had a clear role — time, space, memory, willpower, and emotion. Giratina was just sort of there. And the explanation that it lived in a parallel dimension that was integral to the existence of the real world when it was so small was pretty strange. Then Junichi Masuda clarified that Giratina was the personification of anti-matter, and now it all makes perfect sense. The reason Giratina's world is so small is because of baryogenesis, and the reason it's cut off from anything else is because logically, it should explode if it went to the real world (instead, it just transforms to handwave it not exploding). And its creation by a Pokémon God actually has a purpose and sense. How many series have a God of Antimatter in them?
This also explains why Giratina can only exist in Altered Forme outside the Distortion World: it has to take a new form that won't instantly turn most of Sinnoh into a smoldering crater. The Griseous Orb gives it a finer degree of control over the physical properties of its own body, letting it remain in Origin Forme without spontaneously exploding.
Its battle theme sounds like it makes a few odd notes here and there (such as building up a climax, but never paying off). Rather fitting for the ways Giratina is represented.
It has one of the highest HP of any Pokémon in the game, despite being made of antimatter, which supposedly doesn't seem to give it high health. That's because the antimatter on its body is probably so squishy that it actually absorbs massive amounts of punishment.
Its "Origin Forme" looks like a cross between a snake and a spider because arachnophobia and ophidiophobia (a fear of spiders and snakes, respectably) are the two most common phobias among animals. The same can be said about Giratina's "Altered Form," which looks like both a bat (chiroptophobia) and a centipede (myriopodophobia).
Legendary trios:
There's a tendency to view every group of legendaries in trios, and Giratina is no exception: it fits amongst all the major legendaries in the game as a counterpart. It is counter to the Uxie/Mespirit/Azelf trio as a being of human NEGATIVE emotion, it's a counterpart to Palkia and Dialga as outside either of their realms, 'of everything else' if you will, and counterpart to Arceus as ruler of the world opposite of ours, and its sole inhabitant. Giratina is basically equal-but-opposite every other legendary set in DPP.
The idea that it's a being of negative thought and emotions is its location — the pixies are found normally in three caves that are in lakes, while Giratina is found (aside from the Distortion World) in a cave in a hidden fourth lake.
Speaking of color schemes, Giratina, Dialga, and Palkia are seen as counterparts for Uxie, Azelf, and Mespirit, respectively. Giratina is not nearly as well-known as the other two, Uxie specializes in Knowledge (and it can take it away). Dialga is the controller of time, which keeps moving at the same rate no matter what, and it would take quite a bit of willpower (Azelf's specialty) to keep that up, not to mention, the item used to summon Dialga is the Adamant Orb, and the word "adamant", aside from being an archaic word for diamond, means "never giving up"; willpower (Azelf's specialty) is, by definition, the refusal to give up.
If Arceus is God and created everything, he technically created humans too. Which means that in the Pokémon universe, humans are technically Pokémon too. Which makes the fact that people eat Pokémon (Slowpoketails, anyone?) totally valid.
It also explains why attacks are relatively harmless — we're as tough as Pokémon!
In episode 27 of the original series, Ash says "That Magikarp looks ready for the deli counter.", proving Pokémon are eaten.
It also explains why there are so many psychic trainers as if such an ability isn't uncommon. People are Psychic-type Pokémon. The psychic trainers are the ones who leveled enough to learn psychic moves.
This also explains the Dark-types' abysmally low reputation. Not only are those Combat Pragmatist predators' signature attacks super-effective against us — they are also the only ones completely immune to our signature mind fuckery.
Except humans are much weaker than 90% of the Pokémon, and even then, those 10% that are weaker initially will become stronger than us when they evolve. So humans can be fighters and psychic, but even the most trained human fighter or psychic can't match the most basic Machoke or Kadabra. How does this balance up? With the invention and use of Pokéballs, just like the invention and use of spears, bows, arrows, and other tools are the equalizer for Real-World humans against other animals.
In Sinnoh, there is a myth that says Pokémon and humans were once indistinguishable from one another.
Unreliable Narrator aside, the Pokédex does mention that people have turned into Kadabra and Yamask, so its not completely off the table...
For a while now, people have debated Arceus' pronunciation. In Japan, they say 'ar-SAY-us', whereas in the US, it was dubbed as 'ar-KEE-us'. The 'archeus' (pronounced 'ar-KEE-us') is the lowest astral plane that watches over all of creation.
Why would Arceus (and by extension any legendary) let itself get caught so (relatively) easily? Arceus, being God, is immortal, while us puny mortals get to live 70-90 years at best. It's a fair deal (and admittedly a pretty devious one): you get to "own" God for a while, then after your time has come, he either OWNS you (if some people's beliefs are to be right) or simply sets himself free and continues with His business. After all, what's a human lifespan to Arceus — ever thought of that? Maybe he had been flipping you off all the time, or just wanted to give you the illusion of having caught a GOD FOR REAL! and gloat about it while it lasts. Or, simply put, he took a liking to you and wanted to be pals with you, again while it lasted. As frightening as such a thought could be, it's true — such things can happen in the great scheme of things (provided there's one).
Edging slightly into WMG, but it always seemed a little unlikely that demi-grade Pokémon like Rayquaza or Arceus would allow themselves to be captured by mortal trainers. But some, like Dialga, are essentially described as literally the element they represent (e.g.: time). It seems more plausible that the Pokémon is a mere fragment of this god made in flesh and gifted to a worthy trainer. It explains the abundance of the non-event ones, at any rate.
Not to mention, you did help save the entire universe from Cyrus. Arceus would owe you some gratitude...
It's possible that like the Doctor, Arceus travels with a human companion so it can see the wonders of the world through their eyes, instead of just looking at the whole canvas as nothing but a picture.
Turns out Arceus themself confirms in Pokémon Legends: Arceus that what we battle and commonly see/represent them as is just a fragment of their power.
The Poké God Arceus' appearance has been likened to that of the ancient Chinese and Japanese mythological creature Qilin (Kirin in Japan). Why choose that creature instead of an obvious choice like a dragon? According to The Other Wiki, the Qilin in Japan is regarded as the most powerful creature in mythology, even more than the phoenix and dragon.
Some brilliance on the starters' final forms: Torterra, Infernape, and Empoleon all have typings that make them very effective in Sinnoh's incredibly mountainous environments, and all three are Pokémon that are species in real life that are very adaptable or hardy. Not to mention that the final forms all can learn, at minimum, 3 out of the 8 Hidden Moves that don't require flying or swimming.
At 140 out of a maximum 255, the Sinnoh lake guardians have the highest base friendship out of all Legendary Pokémon — or all Pokémon in general, only tying with select evolutionary lines — meaning that unlike other legendaries who start out distrustful, Uxie, Mesprit, and Azelf start out liking you significantly more than most other caught mons do. It makes perfect sense that they'd be so ready to trust you, since you were the one who released them from Team Galactic's torture (the descriptions make a point of stating that they're suffering). Moreover, in other games, the non-boxart trios are usually detached from the main storyline and don't have to be saved by the player in the same way the lake guardians are. Doesn't entirely explain how they still start out with 140 friendship when you catch them in Unova, but it's something.
There are two ways to look at the Unova thing. If we build off of the "relationship to Sinnoh player character" thing, we could say that seeing similar qualities to that person in other trainers is an instant way to endear yourself to the guardians. On the other hand, the high friendship was simply because, as the governors of spirit, their ability to connect with and understand other beings right away is superior to that of most other Pokémon — and the player characters are almost always supposed to be exceptionally good people.
Shaymin is said to be the gratitude Pokémon because of its association with angels.
Upon evolving into Gallade, Kirlia's stubby, spike-like legs turn into actual (if simple in anatomy) feet, complete with visible toes. Why? Because of Gallade's reliance on his shoulder swords. All other members of its line use magic-like, arcane, and/or psychic attacks that don't require the user to have particulary good balance, as long as they can focus on what they're trying to do. Gallade, on the other hand, is a swordsman (or swordsmon) — and good footing is very important in fencing.
Why are Bronzor and Bronzong a teal (green when shiny), when their names are derived from the word "bronze"? It's likely that it's bronze-like coat oxidized, giving it its familiar sheen.
(which isn't actually a bagworm). Although, the debris that plaster bagworms use isn't made of metal, but spiderwebs, fabric, lint, and even hair.