My other favorite (one I'm sure has been mentioned here a few times) is the fact that pokemon eggs are not "really" eggs, something iirc mentioned once a million years ago in that untranslateduntilrecently pokedex book and then one (1) more time in a random ass NPC in XY
It's been mentioned three times in the games according to Bulbapedia (well, two and alluded to in the third case):
According to a girl in Solaceon Town, where one of many Pokémon Day Cares are located, no one has ever seen a Pokémon lay an Egg, and thus, it is not confirmed that this is how they appear. According to Professor Elm, as quoted by a man in Hearthome City, and a Monsieur in Coumarine City, Eggs are not actually eggs and are more like "cradles".
Here's are screenshots of the Monsieur in XY and the girl in Solaceon Town in DPPt:

(I checked Bulbapedia's Quotes page for Professor Elm but he never mentions this, unless I missed something. Maybe the missing screenshots of the man in Hearthome mentions he heard it from Elm and that's what they're referring to. Maybe said man is in BDSP (as well as the above girl in Solaceon Town)?)
I mean, it's weird certainly, but on one end I KINDA get it. There are many mammal-based Pokemon, why are they laying eggs? Not to mention, Pokemon don't only breed within their species but rather there's this cluster of "Egg Groups" which lets all sorts of Pokemon "breed" with one another no matter how different in species they are. Oh, and that's also not to mention Pokemon based on objects & elementals & who are genderless are also able to produce "Egg" even if it requires a Ditto. Infact, Ditto itself is odd as, it's not only able to "breed" with a genderless creature and produce an "Egg" but also Ditto are just supposed to exactly copy what they see... yet no matter the gender an "Egg" is produced (and for Pokemon which are male only (and don't have a female counterpart) that's the ONLY way to get an Egg of their species). So, I can understand GF thinking "you know our "Eggs" are REALLY weird, not to mention the concept of breeding Pokemon kind of leaning on mature content, how about we step away from that and say not only have no one seen a Pokemon lay an Egg but they're also not Eggs in the typical way we think of them; they're just called "Eggs" because that's the closest comparison people could make".
"Then what are they then"
"They're, um, like cradles..."
... And since I brought it up in a recent thread, I too knew of this little oddity fact and so decided to play with it by including at least a part of it in my PokeMatter theory. Taking what the NPCs are saying at face value, Pokemon indeed don't lay eggs, infact the way Pokemon propagate is completely alien to humans (and real world animals). Pokemon have found a way to form an energy union with an accepted partner which then a PokeMatter shell is constructed around (note Pokemon don't have to like each other to do this, they just need to agree that the other Pokemon's genetics would make a good pair with theirs; this is also likely only to happen with trained Pokemon as Wild Pokemon would likely stick with their group. BTW, as sick as it sounds, this also explains away how you can "breed" family members together: you're technically not as it's just energy being contributed). This union sort of happens in both its own plane of existence as well as absence of time; while the Pokemon forming the union it'll feel like it takes however long they perceive to take, from an outside view one moment two Pokemon are standing together, next there's a Pokemon Egg. Infact it's so instantaneous the outside viewer's mind simply assumes the Egg has always been there and it just didn't notice it right away. So, the Egg itself is just a bundle of two compatible Pokemon's energy within a PokeMatter shell (the theory I link to more goes into how Ditto does it, since Ditto is only contributing a copy of the same energy it's technically not compatible but Ditto is also able to artificially construct a PokeMatter shell, thus when you breed a Pokemon with Ditto you're sorta cloning it). From there is just sort of works like a normal Egg, the two energies and the traits encoded in them begin to merge and solidify into the mother's/non-Ditto species (or whatever other exception I can't easily typo out like with the gender counterparts), possibly using the PokeMatter shell in someway to help in that regard as well. As first there doesn't feel to be anything in the Egg cause technically there isn't, it's just energy in a shell, but as it merges it gains a physical presence and thus weight and movement until finally ready to hatch.
I also feel that pokemon being converted to energy/data also works to explain why the first and most prominent artificially created pokemon was done through programming and not e.g. genetic engineering. If we assume the technology exists, it also explains a lot of the weird stuff with items over the series (why they always appear as pokeballs in the overworld, how the player can carry so much, why trade with item evolutions are a thing) and how the teleporters we've had since gen 1 work. I guess if we extend the shrinking thing outwards, it could explain Dynamax and why most large mons are light for their size? Still seems a bit lacking in comparison
Early installment weirdness. Infact Pokemon has a whole page dedicated to it on TV Tropes.
When they first made the games they just wanted to give a reason why Pokemon are able to fit into smaller Poke Balls. So, while not said in-game, their answer was in a booklet explaining that a scientist discovered a certain combination of drugs causes Pokemon to shrink and go unconscious and thus be storable in a container like a ball. For the time when Pokemon was just a game that was enough... then it got super popular. Yeah, this and some older information they wrote they realized wasn't going to cut it if they want to make more games in the future as well as have shows and movies. So for Poke Balls they resorted to magical technology. Now, they're could still be a sense of this origin for Poke Balls but it's now very much downplayed and the specifics likely have changed especially with the existance of Apricorn Balls (heck the origin of Poke Balls is a bit messy itself unless you're liberal what has been said. Drayden says Poke Balls didn't exist when he was a kid, which could only be true if he maybe means the modern day version of the Poke Ball. Legends: Arceus not only implies Poke Balls existed couple hundred years ago, but since some of the steampunk balls are based in Apricorn Poke Balls that would imply Apricorn Poke Balls have existed for even longer).
Obviously the Special/Adventure Manga knew about this thus why is shows Pokemon shrunk in their Poke Balls, which is probably why Pokemon fans in Japan "know" this as many probably read the manga, possibly first before the anime.
Didn't know about this! Some interesting stuff:
Belts Before Badges: Now that makes a lot of sense. Without bias, going to "Gyms" to collect "Badges" would certainly sound strange... but change it to "Dojos" to collect "Belts" now puts the pieces together. The "whipping your Pokemon" with them felt like an odd idea, like why? Did you have to make your Pokemon obedient to you first by whipping them to submission? Did they somehow give your Pokemon a boost of some kind? Eitherway definitely unneeded... though odd that also meant they changed belts to badges. "Well, if we can't cruelly beat a living creature with it, no point keeping it a belt". I wonder if they may ever return to the collectible being belt, obviously not giving you the whipping option, but with GF always trying to do something new could see the collectible award being an easy thing to change; I mean, they did it in Alola with the awards being the Z-Crystals.
World Shaped By A Childhood: Lot's of neat trivia about Tajiri's influence on Kanto & Johto here!
- The idea for Fossil Pokemon came from him being able to collect Fossils when he was a kid (at the cost of the wilderness he caught bugs in got urbanized as he grew older; but it also introduced an arcade which developed his love of video games).
- Cinnabar Island was based on a school trip to Izu Islands.
- The size of Kanto is based on Tajiri's experience of how him and his friends used to ride as far as they could on their bikes.
- He later expanded upon that idea in Gen II with how far he was able to go via train, hence the Magnet Train.
- Remember that beta of Johto's map and how different it was to the Johto we got (and Kanto was pretty much shrunk to one giant city location)? That's because it was meant to be based on ALL of Japan due to riding on the trains allowed him to go all over Japan.
Outdated Tech: As Nokocchi said, Porygon is a joke on people who said 1996 was too late to be making a new game on the Game Boy (especially one time Tajiri was at a barbershop) and was told he should be making games that used polygons. But since you can't do 3d graphics on the GB, he made Porygon as a "take that". Not sure why he thought everyone would get the "joke" that Porygon was a "take that", like that's an inside joke only those who kept telling Tajiri to make a game with 3d graphics would get. Most people just thought it was at most an interesting Pokemon concept.
The Planning Days: A bit of a timeline:
* Tajiri pitched Pokemon to Creatures Inc (then Ape Inc) in 1990 and finish it in 6 months.
* Creatures was actually making a similar game called Toto (which uses the GB as an insect cage to catch creatures), but out of respect for Tajiri, cancelled it. They were worried that Tajiri would get offended with Toto feeling they copied his idea.
* Pokemon grew bigger and they couldn't finish it in 6 months. Miyamoto liked the idea of the game and how it could only work on the GB (because of the Link Cable), but didn't want it to be an RPG (of course he didn't...). Miyamoto wasn't sure if they made an RPG they would know "when to finish" and only wanted to focus on the essence of the game. Thankfully it was Tajiri's decision in the end who wanted it to be an RPG. Though at the time of the interview Miyamoto said he still wasn't sure it was the right call.
So, was making Pokemon an RPG the right call? YES. A major appeal of Pokemon is that sense of progression of leveling, evolving, and teaching new moves. Not to mention just monster fighting would feel pointless without a story to give a sense of purpose of doing so. It also gives a chance to make interesting human characters and give them some backstory instead of just being a boss to fight. I feel those are the main points why Pokemon needed to be an RPG at first and no other genre would have really allowed that engagement.
Fuji Forest: OH JEEZ, they were going to include a location based on the Suicide Forest?! Yeah, I could see why it got cut... though I got to also question their thought that would be where Misdreavus and other Ghost-type Pokemon would be. According to Wikipedia, the reason it's believed to be haunted is because of the suicides. Like if there was any religious or mythical connection to it being haunted I would think it would have been mentioned (like possibly the practice of ubasute, leaving elders to die, was done there and its haunted by their ghosts, but I feel that's overshadowed by the modern day mass suicides). So including the Ghost-types there would have been SUPER inappropriate.