The design of Rotom is a throwback to the design of Pulse-Man, a game previously made by Game Freak.
Everyone knows how Nintendo's former rival Sega has gone Multi Platform after the death of the Sega Dreamcast (and thus has games on Nintendo consoles), right? Well, very little know that the opposite is true in Japan, as there is a Pokémon game on the Sega Pico. (And yes, the Pico is still very much alive over there.)
Gen II: Ho-oh, via cameo in the first episode of the anime. Togepi was the first identified as such however. Donphan also appears in the original film while Marill and Snubbull were in the short film tied in to that and Elekid, Slowking, Bellossom and Lugia in the second. There was also an episode where a sketch of the top of Elekid's head was shown.
Gen III: Kecleon, Wailmer, and Azurill
Gen IV: Munchlax, then Lucario, then Bonsly, Weavile, and Mime Jr.
Bonsly had the honor of actually being playable to a limited extent in a Pokémon RPG before its own game was released — it was available in the bingo mode of Pokémon XD.
Gen V: Zoroark and Zorua
Gen VI: Chespin, Fennekin, Froakie, Xerneas and Yveltal
Rhydon was the first Pokémon ever created, according to Ken Sugimori. You can see this in Red, Green and Blue's code - the internal list of Pokémon starts with Rhydon. Second is Kangaskhan.
Which might explain why some variations of Missingno. turn into Rhydon at some point and the Glitch Pokémon 'M can actually evolve into Kangaskhan.
Mew was copyrighted in 1990 by Game Freak, years before the release of Red/Green.
Despite this, Nintendo didn't even know that Mew had been programmed in by Shigeki Morimoto when Red and Green were released.
Pokemon Red and Blue weren't the first Pokemon games in Japan. Over there, the duo was originally Red and Green, while Blue was a third game that was pretty much a remake with better graphics and a few bugs fixed.
When they were imported into the United States, Game Freak took the Pokémon lists and scripts from Red and Green and programmed them into Blue, giving us remakes of Red and Green with the improved graphics of Blue.
Incidentally, this is why one of the NPC traders tells you that your Raichu evolved after you trade it to him (Raichu cannot evolve)—they took that line from the Japanese Blue Version, in which you trade him a Kadabra (which evolves into Alakazam when traded).
This is also the cause for the infamous Green vs. Blue naming of the Rival who later becomes the Gym leader of Viridian. In Japan, the Rival is originally known as Green to the main character's Red. However, since the improved Red and Green versions were released as Red and Blue in America, they wanted to be consistent with your player being one version and your rival the opposite. Many fans argue over which name you should use when referring to Green/Blue/DOUCHE (you DO have the option of naming him in-game despite default canon), while others simply say "whatever."
If a shiny Ditto copies a regularly-colored Pokemon, it will transform into the shiny version of that Pokemon. If a regular-colored Ditto copies a shiny Pokemon, it will transform into the regular-colored version of that Pokemon. And, somewhat-obviously, if a shiny Ditto copies a shiny Pokemon, it will be the shiny variant.
Or at least this was true in Gen III, in the Gen IV games this doesn't work and a shiny Ditto changes into regular-colored Pokémon.
There's an exploit abusing this in Gen II and Gen I. Simply transfer the shiny Gyarados to any Gen I game, and capture a Ditto after it transforms into that Gyarados. Voila, transfer it into any Gen II game and you have a shiny Ditto. And because of the way the game is structured, said Ditto vastly increases your chances for a shiny egg of any other Pokemon when breeding with it.
Currently, Pokemon Ranger: Shadows of Almia is the only Pokemon game in which you can actually die (Specifically, by failing to stop a sinking ship.).
In Guardian Signs, there is a similar mission, except instead of stopping a sinking ship it's escaping a flooding submarine.
The favorite Pokemon of Satoshi Tajiri, the creator of Pokemon, is Poliwhirl.
Suddenly, Red from the Special Manga having Poliwhirl as his first Pokémon makes sense.
And so does a Poliwhirl randomly appearing in a Pokémon Zensho artwork.
As does Poliwhirl randomly being a Pokemon trophy in Super Smash Bros. Melee despite not appearing in the game either as playable, from a Poke Ball or any other way.
Also probably explains why Poliwhirl was the cover Mon on Time magazine once.
Think you've got a guaranteed catch with a Master Ball? Think again; thanks to how catch rates are calculated in the game, there is a slim chance of the Master Ball failing. How slim? 1 out of 65536. That's eight times less likely to happen than encountering a shiny Pokemon.
Don't know about the Gen. III games, but this is not true in the Gen. IV thanks to an early check in the formula. However, if you don't pass this early check but would still have a "100%" chance of capture, you do have a 1/65536 chance of failure.
Longtime fans may remember back in Generation I when bogus rumors were flying about the infantile internet speculating on a possible secret/glitch that would allow you to catch the most elusive of all Pokémon: Mew (No.151). Surprise surprise, there really IS a secret glitch that allows you to catch a Mew! For real this time! Now the bad news: you will probably have to restart your game in order to pull this off, since the easiest method for getting Mew requires you to have not battled a certain trainer on the route north of Cerulean City. Mew is actually only a small part of a game-breaking glitch which can be activated as soon as you have Teleport/Fly and meet a trainer who will try to battle you as soon as he appears on-screen (near Lavender/Saffron). Fly away before he battles you, but after the "!" appears over his head, and you will soon find yourself battling strange glitch Lv.7 Pokémon determined by the Special stat of the last Pokémon you fought.
Junichi Masuda's favorite Pokémon is Victini (it used to be Pichu), favorite type is the Water type, and favorite move is the Water-type Surf.
In an IGN interview, he also mentioned Tangela as one of his favorites. He said he liked how it evolved into Tangrowth and considered it underrated.
Cryogonal and Mew, despite being genderless Pokemon, can learn Attract and use it on other genderless Pokemon.
Fan Nickname: TrollFreak for Game Freak, thanks to their(extremely) questionable mechanic changes and implementations of the games itself. This is, by far the most used nickname in pokemon community, both for casuals and competitive players.
Hey, It's That Voice!: The anime was dubbed by 4Kids after all, though the TPCI dub does have its share once DP got going.
Toho often helps put together and distribute the anime, especially the films, and anyone familiar with the Godzilla series will recognize some of the Pokémon roars and cries as being from the ranks of Kaiju. Giratina has Adult Mothra's chirp, Palkia uses a mix of Godzilla 1954 (in Super Smash Bros. Brawl) or Heisei King Ghidorah (in the anime) and Boga the varactyl's warble, Dialga's roar is a higher-pitched variation of Gorosaurus, and the "Megarig" vehicle uses Megaguirus' shrill keen.
Also, Sean Schemmel, of Dragon Ball Z fame, has appeared multiple times throughout the anime, as Archie, Cyrus, Grings Kodai, and Lucario.
In the Japanese version of Best Wishes, Taiki's Voice Actor took up the role of Luke (The guy who made movies and has a Zorua).
The episode that introduces Elesa is a Yu-Gi-Oh! 5Ds reunion, with the gang meeting Bianca's dad. It's harder to tell early on, but when he goes all Hot Blooded, you almost expect him to say "Let's rev it up!". Biana is voiced by Bella Hudson (Akiza Izinski), while her unnamed dad is voiced by John Campbell (Yusei Fudo). Also, his Japanese nickname is "Red Shooting Star", which could reference Yusei's "Shooting Star Dragon''.
Celebi has a bad tendency to not get released in the US. Only three US events - one in Gen II, one in Gen III that only made it to ten cities, and another near the end of Gen IV - have given it out.
Trolling Creator: Game Freak for mostly the same reason as their nickname. What can you say when they made Levitate Flying Rotom, and Insomnia Delibird, or Event Only Heatran with Eruption and Quiet Nature ?note Eruption does damage based on Base Power x (Current HP/Max HP x 100%). Such moves are generally paired with Choice Scarf(increases speed by 50% at the cost of using only one move) for a fast and powerful combo. Quiet Nature is a nature that lowered speed
Apparently, Shellos and Gastrodon were intended to be in Pokemon Ruby And Sapphire versions, but they weren't integrated into the final design, according to a Nintendo Power interview with Ken Sugimori.
Stunfisk was originally going to be a Water/Electric angler fish, but was changed to increase type diversity within the Unova region (and possibly globally, seeing as we already have Lanturn).
Dragonair used to have spikes and a different head design. Noticeably, the beta version looks more like Dragonite then the Dragonair we know today, so it's evolution would have been a smoother transition had they kept the old design.