TV Tropes Will Ruin Your Life in action here. Combusken has been described on this site as somewhat... phallic, and it's kinda true. Combusken also happens to be a 3-foot-tall chicken that, like all starter Pokémon, is primarily male. In other words... it's a giant cock. For bonus points, it learns Peck, making it... a pecker.
Gardevoir looks feminine, but can be both genders. And its/"her" Pokedex entry suggests that it/"she" will always watch over its/"her" trainer, even if it meant endangering it/"herself." Acccording to Bulbapedia, Gardevoir wasn't intentionally designed to look female.
Gardevoir has the misfortune of being named in the Japanese world as Sirknight. You wouldn't call a feminine-looking Gardevoir as "Sir," nor do they have anything in their appearance (but maybe in their nature) that would suggest them as knightly. Fast forward three generations later with the introduction of the Fairy type, and Gardevoir is rehauled to be a dual Psychic/Fairy type. Fairies notably are the bane of the Dragons' existence, being strong against Dragons and immune to their attacks. Now, what is the specialty of knights in fiction? Slaying dragons.
Bonus points: Gardevoir, as a Psychic type, are weak to Dark types. When the Fairy type was introduced, Gardevoir gained ground against Dark types. Now what does this say about knights? Even if you use every trick in the book, every cheap shot you could hit him with, knights will eventually find a way to combat you and defeat you. As for Fighting types? Well, one should learn that bringing fists to a sword fight is very much not recommended.
Zangoose and Seviper can't be taught how to use HM01 (Cut), even though they have sharp claws, because of their generations-long feud; wild Zangoose have never used their claws for anything but combat, and so they cannot grasp the concept of cutting trees for utilitarian purposes.
Additionally, the move Cut in Japanese is a reference to iaido, a sword-art with noncombatant roots that involves unsheathing the sword, cutting the target, then sheathing the sword again. Zangoose can't learn Cut, because they are always prepared for battle with Seviper and won't "sheathe" their claws. Seviper also, despite their blade-edged tail, cannot learn Cut for the same reasons.
The reason Wailord, a 14.5 meter (47 ft., seven-inch) long whale weighs 400 kilograms (877.4 lbs), roughly the weight of a riding horse, is because it's based on a blimp. It's probably full of air, which gives it an extremely low weight for its size. It's even classified as the "Float Whale" Pokémon.
Swablu, a little bird, goes from Normal/Flying to Dragon/Flying when it becomes Altaria. It's a play on how birds are considered living dinosaurs. And what else have people referred to dinosaurs and their relatives as? Dragons.
Why did Milotic evolve using the Beauty stat at first? It's because "dry" Pokéblocks/Poffins promote the Beauty Stat, and those are preferred by Pokémon with a Modest nature. The Modest nature is valued among Special Attack specialists such as Milotic because it raises the Special Attack stat and reduces the Attack stat (which likely won't be used anyway). It's a nod by the developers that your efforts are better focused encouraging a Pokémon's strongest stat.
Or it's simply to represent the ugly fish changing when it becomes beautiful enough. The reason why the Modest nature enjoys Dry Pokéblocks is because the developers didn't want to make it even harder to get a strong Special Attacker like Milotic.
It may also be a nod to the fact that many people who are considered conventionally beautiful/handsome don't describe themselves as such or they're never satisfied with their looks (just look at how big plastic surgery is in Asia despite being a relatively young industry). It starts life as an ugly fish and evolution involves trying to be as pretty as possible. Even with attaining enough beauty to evolve, its most preferred nature is modest not just due to being a special attacker, but because Milotic may still be self-conscious about how it looks. Assuming it wins all contests in the Beauty division, it may wonder why and still see itself as an ugly little fish and not a rainbow-colored serpent.
Dark-types are usually cruel, but Absol warns people of disasters before they happen. The 'Dex says that since they were easy scapegoats for the disasters, people hunted them down. In order to protect themselves, they developed more vicious moves, which is why they're Dark-typed. But they never dropped their old habits.
Furthermore, the Pokédex was created by humans. Because people thought Absol was causing disasters instead of warning people of them, it was classified a Dark/Evil type.
...Except that classification by type in natural (based on actual, obiectively common features) and not artifical (based on subjective features considered common by humans), as evidenced by all Pokemon of the same type sharing common strenghts and weaknesses (unless they're neutralised by an ability or secondary type). Absol isn't classified as a Dark type because humans consider it evil - it's classified as a Dark type because it IS a Dark type.
Absol has all the Dark type's strengths and weaknesses because it's so desperate to prevent the disasters it foresees that it becomes a Combat Pragmatist, one of the Dark type's defining traits.
One of Absol's possible abilities is Super Luck, allowing it to crit more easily. Flavor-wise, the ability normally implies the Pokémon being Born Lucky and thus more prone to getting lucky hits on opponents. However, Absol's precognition allows it to predict the opponent's movements and hit them where it hurts more easily, which makes it look like it's getting disproportionately lucky to the untrained eye.
Whenever you catch a Luvdisc, they'll be holding a Heart Scale, which you can put in the bag and trade. Certain fish (goldfish spring to mind) drop their scales if they have been in a fight. Handily providing a good explanation for why you can find Heart Scales at the sea bottom Luvdisc would probably be fighting in the depths, and not all trainers on a grinding spree would care about collecting the dropped scales!
The Whismur line has Soundproof as their main ability, despite having Make Me Wanna Shout powers. However, it's possible that they scream so much that they deafen themselves. Loudred's Sapphire entry even states that it goes temporarily deaf after shouting.
Kyogre has type advantage over Groudon, when they're supposed to be equals in strength... except they aren't supposed to be equals in strength: In their battle years ago, Kyogre created the ocean, while Groudon created the landmasses. Now, what is there more of on Earth's surface, continent or sea?
Groudon and Kyogre have the same base Speed stat, so it's a tossup as to which one would strike first. Both could get Super Effective hits on each other. They are almost completely evenly matched.
The move Groudon uses in order to KO Kyogre is the special, Grass-type Solar Beam. Kyogre can use any Water attack or Ice attack to KO Groudon. Not to mention that Groudon is playing off its weaker Attack stat and Kyogre's stronger Defense stat and doesn't get STAB, while Kyogre is getting the better end of both conditions. Groudon is still pretty much screwed against Kyogre.
Hoenn having more water and surf routes than any other region and the amount of land and water more even than most other regions can be explained by Kyogre and Groudon fighting for dominance over the region.
Gardevoir is a Pokémon known for being, even by Pokémon standards, highly devoted and protective of their trainers. Now, what happens if an abusive trainer (Paul for example) had a Gardevoir?!
The official Pokédex text describing Spoink says it "bounces around on its tail. The shock of its bouncing makes its heart pump. As a result, this Pokémon cannot afford to stop bouncing if it stops, its heart will stop." What do you think will happen when it faints in a battle? Or worse, when it's been Paralyzed in battle?
In Pokémon Mystery Dungeon: Explorers Of Sky, a Spoink says that he's lost his pearl, and without it, he's bouncing unpredictably. Since bouncing is what makes their heart pump, erratic bouncing is causing irregular heartbeat which the pearl is there to balance out!
A Groudon's weight is around 2100 lbs, or 950 kg. It uses Stomp on a Skitty. Splatz.
Skitty is in the same egg group as Wailord, meaning it can breed. Either way, Skitty loses.