Ascended Fanon: The fan theory that Giovanni and Team Rocket had some connection to Mewtwo (whether it be in its creation like in the anime and Pokemon Adventures manga, or as what they wanted to capture when they gained control of Silph Co. and its Master Ball) has been given credibility with Giovanni possessing Mewtwo in Ultra Sun and Ultra Moon.
Remade for the Export: The international releases were based on the Japanese Blue version, which fixed a number of glitches and had a host of graphical improvements, particularly to the battle sprites.
Sleeper Hit: Nintendo of Japan thought the games wouldn't do well while releasing Japanese Red and Green and wrote them off as a loss. They didn't top the sales charts, but kept selling steady in a market where 80% of sales are made in the first two weeks. Game Freak made a few tweaks, released an updated version (Japanese Blue), and Nintendo got their cash cow.
There's a creepypasta about a hacked version known as Pokémon Black (not to be confused with Pokémon Black and White), found on a black-painted cartridge. The player is given a Pokémon known as 'Ghost' instead of one of the starters, and it cannot be put into the PC. It attacks opponents with Curse, and if you return to an area after beating a trainer, it's indicated they died as there's a tombstone present. After beating the game, the player character's Pokémon are all gone and the sprite is swapped for an old man sprite. Going back to Pallet Town results in the character being attacked by the spirits of the Pokemon they killed on their way to beating the game, with the character using Struggle until they die. Its existence is questioned, but a ROM like this does exist online. Article here
Missingno. (or Missing Number) has had a number of rumors around it, some said catching it would damage your cartridge others say that it would erase your data.
There's a truck sprite that only appears once in the game. The only way to see it is to go way out of your way to avoid triggering a certain plot event that closes off the area and returning when you can travel on water. People believed that it had to have been put there for a reason, leading to hundreds of rumors about this thing. As it turns out, it's just a graphical easter egg with no actual benefits associated with finding it. As a reference to these rumors, in FireRed and LeafGreen, checking under the truck gives you a Lava Cookie.
There are various rumors about how to catch Mew, many of which involve moving the truck in Vermilion City in some convoluted fashion. While it is actually possible to catch by abusing glitches, none of them involve the methods perpetuated by the popular rumors.
Speaking of Vermilion City, the S.S. Anne was said to return there after the player beat the Elite Four so many times. There is actually a way to re-enter the S.S. Anne through a glitch, but it does not involve beating the Elite Four in any way.
Some old cheat lists claim that your Mons will receive a "revenge boost" to their Attack when their other stats are decreased. This one is actually partly true; while nobody intentionally programmed that feature into the game, one of the game's myriad bugs causes badge boosts to be reapplied every time any of their stats gets modified. That said, any move that modifies a stat will force a proper recalculation of that stat, wiping away these glitch boosts. It's not revenge, it's just a glitch.
There once was a female protagonist◊. She was excluded presumably due to a lack of space for her data and reused for FireRed and LeafGreen as "Leaf". Her design was used for the character Green (known as Blue in Japan) in Pokémon Adventures.
There were originally going to be 190 Pokémon, but they were cut for space, leaving 39 instances of Missingno. in the vacated data slots. According to Bulbapedia, all 39 of the cut Pokémon would later end up in Pokémon Gold and Silver. This explains the lack of Suspiciously Similar Substitutes in Generation II, as many of them were made alongside the originals. Strangely, Ho-oh was not part of the original planned roster of 190 Pokémon, despite appearing in the first episode of the anime.
Originally, Mew was not planned to be programmed into the games as an actual Pokémon at all, despite being mentioned in several texts in the Pokémon Mansion. Shigeki Morimoto only slipped Mew into the code just two weeks before the games finished development.
During development, the Sevii Islands were considered. But, due to a lack of cartridge space and time limits, they were dropped. They were added in the remakes FireRed and LeafGreen.
Trainer battles were originally going to trigger every time you entered line-of-sight instead of just the first time. Pokemon Breeders in Pokémon Black 2 and White 2 would exhibit a similar behaviour.
Professor Oak was going to be battled at some point late in the game. He uses a high-level team that's very similar to Blue's final one and includes the fully evolved form of the starter that wasn't picked. The data is still in the game and he can be fought via glitches or a cheat device. This unused fight later served as inspiration for the Champion battle against Professor Kukui in Pokémon Sun and Moon.
The HMs were originally going to be normal TMs that could be purchased and sold just like the others.
Looking at the index numbers of the HMs reveal that there's an empty slot between Fly and Surf, suggesting that another was planned but never implemented.
The ability to travel across water was originally allowed by a key item instead of a field move, and didn't require any Badges to use. It's entirely possibly that this was meant to be a debugging tool, as it's called "?????".
Many Pokémon had different names planned for them in the English translation. These changes range from minor (i.e. Pidgey was going to be Pidge), slightly different versions of their original names (i.e. Kakuna was Kokoon, a corruption of its Japanese name Cocoon), completely different names (i.e. Tentacruel was Man O War), or direct translations of their original Japanese (i.e. Chansey was going to be Lucky).
Some concept art of the Gym Leaders Tweeted by Ken Sugimori labels them offset by one digit (Brock is 2 instead of 1, Misty is 3 instead of 2, etc.) with Viridian's in the first slot, suggesting that the original Gym order would have the player challenge Viridian Gym first instead of Pewter Gym. There is also artwork of unknown young male alongside the other Gym Leaders, implying that Giovanni was not originally intended to be the Viridian City Gym Leader.
The localization team considered beefing up the Mons, on the grounds that American audiences might not take well to "cute monsters".
Trivia for Yellow:
Keep Circulating the Tapes: An even more severe case than the originals, since at least those were remade for the GBA. Rescued along with the originals on the Virtual Console.
Recursive Adaptation: It's a game based on The Anime of the Game, and in addition to some Canon Immigrants, there are some touch-ups on sprites and Pokémon used in Gym battles: Brock and Misty wear their respective outfits from the anime (in the original games, Brock was shirtless and Misty wore a bikini), and Lt. Surge only uses Raichu in battle, which is what he also did in the anime.note He used 3 Pokemon in Red and Blue, and the remakes and later games follow this instead.
Trivia for FireRed and LeafGreen
Fandom Nod: As a Shout-Out to the aforementioned truck rumor, the pier that the truck sits on contains a Lava Cookie, which are normally unavailable until you reach the Sevii Islands.
Fan Nickname: The name "Leaf" for the female Player Character has never been stated to be her actual name. It is based on one of the placeholder names on the ROM for FireRed and LeafGreen.
Too Soon: The model of the space shuttle in the Pewter City Museum is no longer referred to as the "Columbia" anymore, most likely in response to the destruction of that particular space shuttle in the year prior to the remakes' release.
Urban Legend of Zelda: It's said that if you have a fake copy of the game, or if you play the game in a very outdated emulator (preferably, one that was released before the game itself), the Seagallop ferryman in Vermillion City will say "By the way: If you like this game, buy it or die." This message is actually only in some very early ROM dumps of FireRed, and in reality, was the work of the pirates who managed to leak the game early.
What Could Have Been: LeafGreen was originally considered to be retitled to "WaterBlue" for the international releases to match how Red and Blue were the versions released outside of Japan instead of Red and Green. However, it was ultimately decided that the international releases would be titled the same as the Japanese release, as the Leaf in the title was supposed to symbolize peace in a world of friendly competition, and they also did not feel like redesigning the box art.