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Wild Mass Guessing specifically related to the Meta Guessing for the Pokémon franchise. For other Pokémon related WMG's, see Pokémon.
Please add new entries to the bottom of the page.
The Pokemon world is in another universe.
Details from Black and White reveal that a season occurs every month. January, May, and September are Spring; February, June, and October are Summer; March, July, and November are Autumn; and April, August, and December are Winter. This must justify that the Pokemon world is in another universe, and that their Sun might be much smaller than ours.
PokčEarth is in our far future. And Mystery Dungeon takes place in an Alt. Timeline.
Simply, Earth is enveloped in Nuclear War, and everything is mutated by fallout into Pokčmon.
Echidnas -> Cyndaquil Line Hedgehogs -> Shaymin Snakes -> Ekans, Arbok, Seviper, etc. Horse -> Ponyta Camel -> Camerupt So on, ad infinitum. The humans in PokčEarth are descended from survivors with Rad-proofed bunkers. Those without bunkers became Tyrogue and eventually the HitmonGang... and Ralts/Kirlia/Gardevoir/Gallade... and Jynx... and the rest of the Humanshape egg group. For every culture there's a religion, so Arceus just happened to be the most Jesus-like Pokčmon, resulting in a religion based around a mutant horse-deer-thing. However, for the Mystery Dungeon games, there simply 'WERE NO BUNKERS'.
The Pokemon World is an alien planet.
It's home to life that's very close to earthly organisms...but not close enough. Its year seems to be a quarter the size of our own, since (as of Gen V) seasons only last 1 month. Not to mention the Pokemon world's geography, which includes what looks like England, a split Europe, 2 Italys and 2 Scandinavias. Humans, therefore, must be colonists, who have been on this planet for a long, long time.
Ash is the embodiment of every hero.
Every hero in all fiction is the same person, and he's just this one. Think, all the heroes are winners, have tragic backstories, and will have an epic downfall. They go by a thousand names, but they are all the same person. All heroes follow the same patten, from Luke Skywalker to the Cyborg from Marathon. Tragic backstory, becomes the hero, is manipulated by the villain or someone, works with others, and sooner or later, has a tragic end. Ash hasn't hit that last part... yet.
The hero of the Video Games is only a Heroic Mime outside of battle.
When the Player Characters are in battle, they are the ones commentating on the sidelines with phrases such as "It's super effective!" and "PIKACHU is hurt by poison!" The main evidence for this is that Red in Gold, Silver, Crystal, and Stadium 2 cannot speak... because he's tired his vocal chords out from shouting over the past three years.
The player and the player character cannot hear each other.
The show will end in two seasons, in which Ash will defeat the Pokemon league and end up facing either his long lost father, who has become Champion, or a final showdown with an as-of-yet unknown evil character who's been pulling the strings all this time/reveal a conspiracy about Ash and his father.
He'll use his strongest Pokemon from each land (Pikachu, Heracross/Donphan, Sceptile, and so on.). He may also face one or more of his friends, such as Ritchie or Gary. Maybe Paul will show up post Heel Face Turn. (You know that's going to happen. Don't deny it...)
The next Mewtwo-related movie or special will have the cloned Pokémon forming an army.
Look at Mewtwo's track record of specials so far. First we had "Mewtwo Strikes Back", followed by "Mewtwo Returns". His next appearance was in the "Mastermind of Mirage Pokemon" special, but only as one of the titular holographic creatures. In truth, the special should have been called "The Phantom Mewtwo". With this in mind, clearly the next time he appears should involve an attack of the clones.
There is a continuity extending beyond the Pokemon games
Before they created the Pokemon games for Nintendo, Game Freak made a game for the Sega Genesis called Pulseman. Now, as of the D/P generation;
Ash's Pikachu is powered by Shipping.
Okay, I got this idea from a WMG Lyrical Nanoha is to be believed, beings that run on Ship-to-Ship Combat—especially in a world with this much of it—are really, really strong.
Master WGS's Pokemon The Abridged Series is canon.
Just as Yu-Gi-Oh! The Abridged Series is, Pokemon the Abridged Series is the actual show, while the "real" anime is just fake.
Zoroark is based on Set.
If Lucario is Anubis, it only makes sense to bring in the rest of the Egyptian pantheon. Zoroark and Set are both fox-like bipeds with chaotic tendancies and long red hair, after all. Granted, this opens up Unfortunate Implications given what Set has been known to do... Forget it. Half the fandom's embraced it already.
Someone on the production staff reads Mahou Sensei Negima!.
Does anyone else think the "eat your own attack to gain power" trick looks like a Lighter and Fluffier version of Negi's Jovis Tempestus Fulguriens/Incendium Gehennae moves?
There will eventually be fire types that represent the entire Eastern Zodiac
So far we have:
The reason the Leader's levels get progressively harder is because the in-universe metagame is advancing.
It works like this: At the start of any given Pokemon game, you get your Lv. 5 starter and go beat up some Com Mons for a while. At this point, every Pokemon in the game is around the same level, the level of the first Gym Leader. Your Pokemon's level and stats are not its actual, absolute strength but instead is the percentage of its potential power. So your starter is 5% as powerful as it could be, while the Gym Leaders are at around 15% of their potential.
Since your character is crazy talented and destined to become Champion and all, s/he approaches the metagame in a new and innovative fashion, and by the time you get to the Gym Leader your Pokemon are using more of their total power and win the battle. Since news travels fast among Gym Leaders, the later Leaders and the Trainers that trained with them are already using your new techniques against you by the time you get to their Gyms. Even the wild Pokemon learn some new tricks, but without a Trainer, they cannot learn as quickly, and are thus at a lower level on average.
By the time you get to the Champion, they've been following and implementing your innovations the whole game (and inventing a little on their own - there's a reason they're the Champion, after all) and the resulting showdown is far beyond anything the world has seen before, with Pokemon using as much as 60% of their potential.
This all boils down to "after the first Gym Leader, everyone else is copying your ideas and getting stronger that way." It also explains why the Gym Leaders are so much stronger in the rematches in Heart Gold and Soul Silver—they're training at about the same rate as you. Finally, Red's Pokemon are so powerful because he's been working with them for a very long time, and as such knows almost the complete extent of their potential.
Missingno has the ability to make Pokemon incredibly powerful for short periods, going up to 255% potential.
Pokemon is set in Valhalla.
Exactly why are Pokemon so willing to fight, anyway? They have nothing significant to gain, and it's obviously painful, so why do they do it? Simple: They are the souls of dead warriors, and Pokemon trainers are the souls of dead commanders.
Trainers don't get hurt because generals don't participate in battles. When you catch a Pokemon, you prove your tactical acumen to it. Nurse Joy is a Valkyrie.
ONLY the audience sees Team Rocket wearing Paper Thin Disguises...
...however, Ash and co. don't because Team Rocket actually puts on rather decent costumes. It's for Rule of Funny, or like a kid's show: they make it easier for the audience to understand things. If this didn't happen, then you would confuse Team Rocket for any character of the day.
Blue (the girl) writes for the anime.
That's why none of Ash's bird Pokemon get much character development or screentime - she still suffers a little bit from bird Pokemon. She related Ash's birds to the one that kidnapped her when she was a child. Plus, Ash saw Ho-Oh...
Red becomes Pulseman.
After the player defeats Red on Mt. Silver, Red leaves. With a high level Pikachu. Red, influenced by the design of Rotom (this assumes he visited Sinnoh), creates an elaborate backstory for himself as Pulseman. He learns to link himself online with the help of a Porygon and has Pikachu create the electric attacks. So Pulseman is actually a Henshin Hero of sorts. Doc Waruyama fooled himself into thinking he created Pulseman, and picks up some Team Galactic grunts to reform the Galaxy Gang. Everything about Pulseman was made up by Red... 'cause he's Red.
The whole Pokemon universe is actually a video game but Ash doesn't know.
Ash is really in a video game world. This would explain why npc like Nurse Joy and Officer Jenny are the same in each town. The programmers were either taking a short cut or they were trying to create popular characters that could act as mascots for their game. The fact that ash does not consider their identical-ness odd implies that Ash does not realize that his world is a construct. This can also explain how Pokemon can be stored in balls and pcs. Pokemon are only bits of code that have no real physical form. Their digitalness is showed when they are placed into a ball and they become a red light. The lineal deign of the Pokemon world also shows how it is a game. Gym leaders tend to have stronger Pokemon as Ash's journey goes on. This is because the game Ash is playing is meant to be solved a certain way. This theory also explains how new Pokemon and new areas are discovered. Ash's world is simply receiving an expansion pack.
Pokeballs use Element Zero to store Pokemon.
Using the mass changing qualities of Element Zero, this allows Pokemon like Groudon and Snorlax to be stored in Pokeballs without a significant weight effect on the trainer holding the Pokeball.
The space station in Mossdeep isn't a space station
It's a radio tower.
Explains how you have the Hoenn sound without any apparent radio tower in the reigon. Also, how nothing is on the computer screens, and why you never see the shuttle launch.
Why would they do this? Radios are illegal in Hoenn. Ever since the radio signal incident near the Lake of Rage, they've been outlawed.
Think about it- there's water everywhere. If a lot of sea serpents went on a complete rampage...
Pokemon and their abilities and types come to be through Pantheism
Pantheism is the belief in Eastern cultures that everything has a soul, be it inanimate objects, or animate objects. In other words, "God is the Universe, and the Universe is God". In some Oriental cultures, there are some Oni (Demons), who manifest from forgotten items. In other words, Pokemon like Voltorb and Klink are Pokemon who are born when power manifests in the object they represent (a Pokeball, and gears).
A single Pokemon can be under the effects of every special condition at once
Under the rules of the video games, A Pokemon can only be effected by 2 special conditions at a time: Confused + Sleep/Paralyzed/Poisoned/Burned/Frozen. However, in the TCG, a Pokemon can be effected with up to THREE special conditions at a time: Poisoned and Burned + Sleep/Confused/Paralyzed. Given that the only two stacks that overlap between the games is Confuse + Burn and Confuse + Poison, it only makes since that in the Pokemon canon, its possible for all 6 Special Conditions to overlap.
Arceus created the Olympus Mons to take charge of his creation.
Think about it. Arceus represents "creator" but not "ruler." This means Arceus would have to create some mons to rule over different aspects of the Pokemon world.
Pokémon is about the world around us, with each Generation telling a different part of the story with a different perspective.
Each Generation tells a story of the world around us, each Generation growing in scale and using a different religion and scope but telling the same tale.
Ash is Giygas.
You cannot grasp the true form of his stupidity.
In Red/Blue, you are the villain.
As this site shows some anonymous Pokéfan elaborating on here: http://nerdbastards.com/2010/05/24/did-you-know-you-were-the-villain-in-pokemon/
The world of Pokemon is our world... in the past
In Diamond, Pearl, and Platinum, Cyrus' plan was to create a world without spirit. Though he was defeated, in Platinum, he promises the main character, "One day, you will wake up in my world." A world without spirit, without Pokemon... We're living it... He succeeded!
The PC actually transports Pokemon to another world.
A world just like Pokémon Mystery Dungeon.
The Pokemon World has something somewhat of a Black History, which contains our history!
Y'see folks, as theorized above, the Pokemon world is the result of a Nuclear Option method of Apocalypse How, and a great war happened to cause massive nuclear explosions, rendering several organisms prone to all sorts of change, and the outcome of this resembles the reaction with animals and humans to the Gene Bombs of the Xorda. Evolution of animals due to exposure, and the populations of human beings decrease to almost nil. Heck, the latter devolved and if this happens, we may as well be Pokemon!
Pokedex entries aren't accurate
Thinking about those pokedex entries, and the, well scary, content of some of them, this troper believes that the entries are written from a rather terrified point in some cases. The trainer, a pre-teen, is sent out to help a professor do research on pokemon. Why the kid is chosen, is because they seem to bond well with their "rare" starter pokemon. For some of the most regular, and least scary, pokemon, pokedex entries might be written, but for the unknown, it might be based on a mix of folklore and a kid not understanding what s/he encounters - which is why pokemon are given such scary attributes in the dex, while not actually being that scary.
Arceus is not God.
If we follow the bible, we can safely assume the obvious: Arceus is a protector, not a creator. However, to protect an entire dimension from evil is asking alot, so he was not only made exceedingly powerful, he was also given many other guardians of these new worlds, who were also given powers. So why, in Pokemon Mythology, is Arceus God? Simple. Ancient humans and Pokemon would have viewed a being of such immense power as a god or just God. He tried to convince them otherwise, but failed.
This would also explain why Giratina was banished. After deciding Arceus was God, the humans needed to figure out who was Satan. Giratina was the most likely candidate, and, despite his protests, they took control of Palkia via Red Chain and banished him to an incomplete world, later called the Reverse World. The Legendaries retaliated, breaking the Chain into three and giving the parts to the Lake Trio.
Don't attack me for taking a religous view to the series.
The Player Character is, in fact, playing a game that eventually became too real.
It's a game of make-believe that a young ten-year-old cooked up in his head. (This explains the wildly unrealistic elements of the game, such as ten-year-olds being in control of fire-breathing monsters). He is chronically shy - the reason he's a Heroic Mime - an makes up for the lack of social interaction by contstructing this fantasy world. The "Pokemon" are just soft toys, or possibly entirely figments of the kid's imagination. The player runs around pretending to become a champion. His mother is fine with this, it's just harmless childish fun. Many other residents play along with the kid (becoming the Gym Leaders and Elite Four) - "Professor" Oak is just a kindly old man who lives down the road. The "region" as a whole is just the town where the PC lives - Pallet Town is his street, Saffron City is the busiest part of town, the Safari Zone is a playpark, Cinabar Island is a big rock in the middle of a pond, etc. Gary Oak used to play with you, but he grew bored of the game and instead resorted to bullying you - it's why he always seems to be ahead of you and has apparenty caught so many Pokemon, he's making it up in order to wind you up. "Team Rocket" are a group of playground bullies who have a problem with the weird kid you pretends he controls monsters and never speaks to anyone. Giovanni is an older kid that acts as a ringleader to the bullies, who eventually takes pity on the poor kid and "disbands Team Rocket" (tells the other kids to stop picking on the PC).
A few months later (which will feel like three years to young children), the kid's mother decides to move house, just to the neighbouring town. However, the PC hates this relocation and withdraws further into his fantasy, constructing a similar yet slightly different identity for himself and everyone around him. Gary Oak becomes more of a Jerkass and starts actively bullying the PC, so he characterises him as the cruel "Silver". The bullies (Team Rocket) continue to harass him, though to a lesser extent. Oak grows more senile in his age, so the PC sees him instead as the bumbling "Professor Elm". He continues to make up new "Pokemon", but remains too attached to the old ones, which is why Johto is filled mainly with Gen 1 monsters. This yearning to regress reaches its pinnacle at the end, where he runs away from home back to "Kanto", and comes face-to-face with his former self (representing his internal battle with his own past). He "defeats" his former self, thus destroying his former childish innocence.
Worried by the PC's odd behaviour, the mother uproots and moves far away to another region. Having lost his attachment to the past, the PC is fine with this, and imagines a whole new world with a whole new set of monsters. He becomes even more isolated from society and instead contstructs the rudimentary figure of May as an imaginary friend. However, he is asked to leave the field where he plays because the "long grass" is in fact a farmer's crops, so he casts the angry farmers in his mind as Eco Terrorists. He sinks further into his delusion, and the line between fiction and reality begins to blur. He is admitted to the mental ward of a hospital, where he meets Wally, a terminally ill boy. He befriends Wally and convinces him that his world is real. Becoming closer to Wally means he no longer needs his imaginary friend, which is why she disappears and Wally replaces her as the rival. However, one day the play-fighting goes too far and the frail Wally is accidentally killed. This horrifying event fractures his mind completely, as represented by the extreme weather caused by Groudon/Kyogre. The PC and his mother are forced to relocate again.
This doesn't help though, and the PC simply falls further into his delusions, his expanding mind allowing him to construct a more complex friend for himself in Pearl. His mother hires a psychiatrist to try and help - Dr. Cyrus, who diagnoses the PC with advanced schizophrenia and an obsessive compulsion to Catch Em All. But the PC does not want to conciously deal with Wally's death and refuses to leave the fantasy world. He views the well-intentioned Dr. Cyrus (who just wants to make (your) world a better place) as a Complete Monster Omnicidal Maniac who wants to destroy his world and everything fun in it. The NPC characters, such as Cynthia, are more involved than ever before because they're not just neighbours playing along anymore - they are the voices in his head telling him that he has to continue his "quest". The Distortion World represented the fractured and crazed parts of the PC's mind which Dr. Cyrus hopes to tame, but eventually he gives up and leaves.
Years later, the PC has grown older but his mind is more broken than ever. Eventually the use of stuffed toys was no longer enough to sustain the delusion, and the PC moved on to capturing and "training" real animals. The NSPCA/some equivalent organisation was understandably outraged by this and demanded his arrest, so he cast them as an Animal Wrongs Group with secret evil intentions. Bianca was just a Naive Girl who wanted to join in the game - her father's objections to her going on her "Pokemon journey" were really him warning her not to get mixed up with the weird, crazy kid. The Yin-Yang legendaries are representative of the two warring parts of his brain: reality .vs. fiction, and he doesn't know which is which any more.
The Sixth Generation games will be set in a high-security mental institution.
The Running Shoes give you Super Speed.
Many players wonder how come you cannot run without specific shoes. However, who's to say you aren't running already, and the shoes simply let you run faster?
The idea is that the overworld, such as the routes, are actually much bigger than they appear. It is simply that the game reduces it. One patch of grass is actually several feet long, for example.
Now, you are actually running as fast as you can at the beginning of the game, but due to the size of the world, that doesn't seem very fast. By putting on the Running Shoes, you are gaining near Super Speed, letting you "run" in the overworld.
By the way, the Running Shoes work like in Pokémon Special, with compressed air giving you a boost of speed.
You don't control single Pokemon.
You control entire populations of Pokemon. Levels are actually entire generations, hit points are individual Pokemon, and learning a new move is simply microevolution.
This explains why the game says that your Pokemon is evolving and not transforming; it's not a single Pokemon turning into another one, it's actually natural selection at work!
Pokemon were specifically designed as battle machines for people.
It's just too convenient that all these strange and wondrous creatures somehow know attacks that humans can teach them. Pokemon were created to be the ultimate battle machines: intelligent, so they could be controlled with a voice rather than a complicated remote control at a headquarters; diverse, so you could select individual mons for every situation; and capable of reproducing on their own so there would be no need to build a new one from scratch if the old one ever got worn out or died; and of course, capable of taking massive amounts of damage without doing anything more than falling into an easily reversible coma. They also could absorb experience from each fight and change into stronger forms as both they and the owner gained more experience. The reason why nobody knows about this is because the original creator of Pokemon died long before any of the game characters were even born, and so they kind of had to figure out how Pokemon worked as they went along. Then they passed the information down to their own children.
Pokemon Trainers are ninjas!
You read this right. Every time you turn on a game of Pokemon, you are actually playing a game about ninjas. No, I'm not talking about Koga (frikkin' fishnet wearing dillentante...), I'm talking about all trainers, specifically the main character. Have you ever noticed, whenever a trainer gets into tall grass, the battle with wild Pokemon's always on their terms. None of the monsters that appear ever gets the drop on the trainer? That's because the trainer always manages to sneak up on the Pokemon well enough so that they have time to pull out the Poke Ball and call a minion before the wild Pokemon can do something reasonable like run away or attack the trainer. Plus if the trainer runs away, they do it completely. There's no running away and leaving a trace for the Pokemon to follow. They run, and then you never run into the same one ever again. Classic ninja. Secondly, have you seen the way they handle Poke Balls? It defies logic. No matter what kind of flair they add before the throw (in the show), no matter how much health the other Pokemon has (in the game), no matter how much a Pokemon resists being captured, the ninja trainer never, ever, ever misses. With skills like that, who needs Pokemon? You could beat trainers with a few shuriken-shaped Poke Balls to the eyes. And then there's trainer battles. I thought it was always weird that the trainer never refuses a challenge, until I realized something. The other trainer saw the main character. Now, the main character has no choice but to take out the dude who saw his face, just like a ninja. And gyms. Just gyms. How do you describe these places? You got a giant building, filled with traps that you have to sneak around, armed guards you have to take out or sneak past, and a warlord (gym leader) whose lair you must reach so that you can defeat him and claim his treasure. Pokemon is really a story about one ninja's quest to invade every ninja stronghold and assassinate every Ninja leader, so they can then go on to beat the legendary Four Ninja Gods (And Gary), taking out all the competition in the process.
The entire world of Pokemon is actually a virtual reality simulation.
The entire world is just a giant video game, created by the professors, and known as such by only a select group of adults. The professors built the game world, and then transported themselves and a small group of people into it, including a pregnant Delia. Ash and company were born there, hence their belief that everything is real. This explains things like how a ten year old boy and his friends can walk alone through a world populated by innumerable wild creatures unafraid; the programming of their world won't let them be attacked. Taking the reality warping a step further, it could explain why no one ages, if living in a virtual world allows you to program a "stop age" into people. All the Joys and Jennys are programs, hence why there are tons of them. Team Rocket is representative of the video game aspect of their world; they represent an antagonistic force for trainers to fight against, even though they are actually completely harmless (since they only harm Pokemon, which themselves do not exist).
Each individual copy of the game is a paralell universe.
Game-link battles and trades are the result of some rather sophisticated cross-dimensional technology, but the engineers of the various Pokémon universes have so far only managed to access worlds which are relatively similar (and therefore must have split from each other quite recently), hence why they have not found any worlds in which Pokémon do not exist.
Pokemon is actually a super futuristic sci-fi game, we just see it as a Mon game
This is based around the assumption that the trainer in Brock's gym is correct when he says that you are 10,000 light years from facing Brock. As you are most likely two squares away from Brock, it can be concluded that each square represents 5,000 light years. The player character must therefore be some kind of interstellar battleship/carrier ship, and the Pokemon are fighters. When you capture a Pokemon, you capture an independent fighter, and crew it with your own men, or somehow convert the current crew into serving you. The reason Pokemon do not die in battles is because the wreckage from the destroyed fighter can be repaired at a licensed "drydock" facility, a Pokemon Center.
Pokemon training is actually an elaborate Alternate Reality Game aimed at young children in the Poke-universe.
Parents of the Pokemon world aren't really letting their young children go off on dangerous adventures. In fact, their kids are only wandering short distances to gain boy-scout-like badges given out by adults at designated checkpoints, in some sort of elaborate community event that combines elements of scouting, scavenger hunts, and electronic gaming. Pokemon are not an indigenous form of life, but holographic virtual creatures scattered through the region for kids the collect and battle. Children are given starter Pokemon for free on a certain day of the year, which marks the start of the event; Pokemon Centers keep track of participants, who are motivated to check in regularly to "heal" their Pokemon.
The virtual nature of Pokemon is already strongly hinted at in the series — Pokemon are digitally transferable, able to learn things from software, etc. Additionally, the alternate reality game hypothesis explains, among other things, why Pokemon Centers are ubiquitous and suspiciously free, why everything is within walking distance and why gym leaders seem more interested in standing around handing out badges than promoting their own poke-careers (it's also strange that even gym leaders who initially seem unkind or "evil" will always play fairly and happily concede defeat when beaten.)
Of course, we're seeing all this from the perspective of the game's 10-year-old participants — the anime in particular represents events as seen through Ash's overactive imagination. Although his fantasies are epic in scope, he's really only playing a game during a few short weeks out of his summer vacation, which is why no one ever seems to age.
The single most fatal mistake one can make in the World of Pokemon...
The first legendary Pokemon to evolve will be...
Lugia. Which will then evolve into Nostalugia, which is just like the old Lugia, but with all the awesomeness of the second gen Lugia.
You, the person playing the games, play the role of a badfic writer. The player character is your Mary Sue / Marty Stu Author Avatar.
This would explain a lot of things. Like why you, a 10 year-old kid, are able to capture legendary Pokemon. And why said legendary Pokemon are perfectly happy to do everything you say and follow you around everywhere. And why random strangers are perfectly happy to give you rare Pokemon and valuable items for free. And why the professors can see you have amazing potential even though you became a trainer about five minutes ago. Heck, we haven't even got to the generation-specific ones yet!
Glitch City is the Distortion World...
...only the portrayal is limited by what the old Game Boy could do. The chaotic nature of reality in both areas baffles the mind, but the DS is capable of showing it without breaking, while the old Game Boy is, uh, not. Its denizens, Missingno. and 'M, are Pokémon that were not known in Kanto at the time of Red/Blue/Yellow, perhaps even relatives or servants of Giratina (it would fit that creatures outside of comprehension would come from a chaotic dimension of antimatter), so neither the Pokédex nor Bill's PC system is compatible with them.
Red and Blue, and/or Ash and Gary, are decended from Cain and Abel.
Your rival always pics a pokemon whose type is strong against yours, because the Gary/Blue character is the one decended from Cain. You/Red/Ash are the decendent of Abel. Except this time you win...
The first four villain bosses are meant to represent the four alchemical elements.
Ghetsis and N in all this... are somewhere in the middle (or perhaps meant to represent Darkness, Darkness and Light, respectively, or some variation thereof).
Norman is the father of all the protagonists.
The father of all the protagonists HAVE to be alive, since they are mentioned as if they were still alive. So, where are their dads? Simple, they all share the same father: Norman. He's a player, married to all the women, and due to the distance between them all, they never find out. In the upcoming R/S remakes, they will confirm this theory after beating Norman. Also, note the badge that he gives out to you, the Balance Badge, which refers to him balancing the love of all the girls. In Gold/Silver, they were originally going to have Red and Gold be siblings, so they had this idea for quite a while. Also, note what TM you get when you beat Norman. Facade.
Effort Values actually have a justification in-game.
A recurring theme with the protagonists of the main games is that they're all incredibly talented trainers, and it's almost always said by someone that the reason they're so talented is that they show love and kindness to their Mons. My theory is that in-game, this manifests as Effort Values (a gameplay mechanic that increases your mons' stats based on the mons they defeat in battle); basically, all of the main game protagonists have a latent psychic ability that forges an incredible bond between them and their mons, which increases the mons' power by absorbing it from the mons they defeat. I don't believe any NPC mons have any Effort Values (or if the games are even coded to have E Vs for wild and NPC mons), hence why you can pretty much plow through most non-Gym Leader trainers.
Legendary Pokemon don't have an egg group because they are still babies.
Mew is the ancestor of Pokemon, it predates every Pokemon introduced so far, even the one who shaped the world into its current mold. The physics of the world were either not yet in place or Pokemon were not able to survive in them, so they sent the egg of Arceus, who either created the setting or shaped a previous world into the current one. It was bred to do it.
Arceus has the highest stat total of any Pokemon right now but Mew has a stat total is not too far off and is a fetus. It is still growing and its adult form will undoubtedly surpass Arceus's current strength. Arceus itself being in the "no eggs" group is also a baby, just a more developed one and so is every other "no egg" legendary Pokemon. Maybe Mew is longer lived than the rest, maybe the other just mature faster, or in Mewtwo's case, were artificially forced to mature faster but each and every legendary in the no eggs group is still a child waiting for puberty to kick in.
Pokemon can breed all over the place because they are all one hyper adaptive genus full of compatible species and subspecies. Most legendary Pokemon are simply stronger, slower growing. less fertile species in this genus who have evolved to ensure the more rapid breeding but more fragile species continue to survive and thrive. Because evolution is random there are few hiccups like Giratina but then, most irresponsible children grow into responsible adults. When they reach adulthood, legendary Pokemon expand their horizons, some already did before Mew and Arceus were born. Alternatively, Mew and Arceus really are among the first but will still mature into cosmic entities and give birth to a new generation that will repeat the process. It would be a fitting end to the franchise should the day come.
Pokemon are the product of a weapons development project...from another franchise.
A long time ago, Nintendo had this video game called Mother, which was about aliens invading Earth. After their failure the aliens went home and came up with new weapons, most notably Gigyas, the result of experiments to increase the power of their soldiers and Mew, from a project working on super powered Tyke Bombs. Gigyas was an uncontrollable failure that destroyed the universe but before then Mew was a complete success and was in the mass production stage when Gigyas lost it.
Seeing Gigyas was bringing about the destruction of the universe, his enemies defeated him by time traveling and changing history in EarthBound. Unbeknownst however is that Gigyas's sister project survived his Suicidal Cosmic Temper Tantrum, creating an Alternate Timeline(he dies in both). Not a whole lot was left, just one baby Mew, some equipment that can still be seen in the hall of origin and an unhatched egg, the last one being why anything survived at all. What would be named Arceus hatched from the egg and it used the surviving data to create more tools and shape a new world to replace the old one.
As guessed above, Pokemon are one giant, hyper adaptive genus with many subspecies. They were bred to be loyal, easy to heal, portable fighting machines which is why they are okay with being contained and battling. There was also data on several flora projects that were supposed to run alongside them. Apricorns were specifically bred to take the monsters in and convert them to energy for storage and repairs while berries were bred to increase their fighting efficiency for example.
Their planet is like Earth is because the aliens wanted them to take Earth. Some Pokemon were based on surviving data, others simply took on forms of naturally developing species then out competed them. Pokemon prioritized on the animal kingdom in particular, the only animals who managed to survive were bugs because of the staggeringly large number of niches they fill and human beings, because of our intelligence. The order to Kill All Humans was lost in the Gigyas incident so Pokemon substituted humans for their original masters and partnered with them. This didn't happen immediately, the human shaped egg group is a collection of failures by Pokemon to out compete humanity before they accepted us as companions. Still, humans are not the masters Pokemon were bred for, so humans must continually prove their worth by catching them.
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