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Pokemon & Science - Did You Know Gaming? Feat. JonTron
 
In the Battle Mansion, the player can fight against a Beauty trainer. After beating her in the English version, her response is "Yes, a mere half year ago I was a Black Belt! Quite the transformation, wouldn't you say?". In the Japanese version, her response is translated as "I was a Karate King a half year ago: the power of medical science is awesome wouldn't you say?!".

Whilst differently portrayed, both versions hint that the Beauty trainer is transgender (black belt is a male-specific trainer class; same for Karate King in Japanese).
Contributed by Castle23clash
The names of Helioptile and Heliolisk seem to stem from Greek mythology. 'Helios' is an ancient Greek titan who is the personification of the sun. Helioptile's Pokemon X's pokedex entry states that it basks in the sun to get energy, strengthening this connection.
Contributed by Cosmonaut
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In Anistar City, there is an old man who is depressed because of the death of his wife. He will ask the player to lend him any Pokemon level 5 or under to keep him company. After defeating the Elite Four, the player can return to the house to find that the old man has passed away, and left the Pokemon behind in a Poké Ball with a letter thanking the player, as well as leaving him a Comet Shard. The letter said how the Pokemon you lent him kept him "smiling until the very end."
Contributed by ChocoPain
X & Y is the first Pokémon generation to add less than 100 new Pokémon (not including Mega Evolutions).
Contributed by Takahashi2212
The reason for the special Torchic Mystery Gift at launch was likely due to the fact that Junichi Masuda's favorite Pokemon is Torchic.

I'm a huge fan of Torchic. I don't know if you saw the intro movie of Pokémon X & Y, but I really pushed to get Torchic in there because its one of my favorite Pokémon. And even back with the Game Boy Advance SP, when Nintendo was making that, I actually made a request to them to make a Torchic-colored Game Boy Advanced SP." - Pokemon X&Y Director Junichi Masuda
Contributed by Zakattack
According to a tourist in one of the hotels in the game, the sixth gym leader, Valerie, is originally from Johto. Given how Valerie also wears a kimono and that her strongest Pokémon is Sylveon, a Pokémon which evolves from Eevee, it's possible that she is related to the Kimono Girls from Pokémon Gold, Silver, Crystal, HeartGold and SoulSilver versions. The Kimono Girls are a group from Ecruteak City in the Johto region who each specialise in Pokémon evolving from Eevee and are always seen wearing kimonos.
Contributed by Akuro
Latios and Latias were found to have Mega Evolutions before these forms were officially revealed by Nintendo.
There are several pieces of dialogue in the game that reference the 3rd Generation games, Ruby and Sapphire. It's thought these pieces of dialogue were references to the 3DS Remakes: Omega Ruby and Alpha Sapphire.
Contributed by Boyobmas
Some time after X and Y's release - and even after the release of the game's official soundtrack - a re-mastered version of the World Champions theme from Pokémon Black and White was discovered in the game's data and decrypted by the Pokémon community.
Contributed by Liraxus
Within the game's files exists three unused sound effects which are all copies of the Pokémon Center's healing machine sound effect. It's thought they were used for testing player-related sound effects during development.
Contributed by Carlos
When battling Mewtwo, Articuno, Moltres, or Zapdos in the wild, a remix of the wild battle theme from Pokemon Red & Blue will play. The remix includes 8-bit portions of the song, seemingly taken directly from Red and Blue.
Contributed by Laikue
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In celebration of X & Y, a short lived Pokémon Center was opened up in Paris, where Kalos was based off. An exclusive Poké Ball-patterned Vivillon was distributed at the store.
Contributed by RadSpyro
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The name "Viola" (the same name as the Santalune City Gym leader) is not allowed as a player or Pokémon's name. This is likely because "viol" translates into "rape" in French.
Contributed by ShinyHunterBN
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The boy band "Union J" changed their names to "Union XY" for one day to celebrate the release of Pokémon X & Y.
Contributed by gamerofgames
There is a Pokémon Ranger that will ask the player to join Pokémon Ranger team, saying that they could be the Blue Ranger. This is thought to refer to the Power Rangers, an American TV series that takes much of its footage from the Japanese tokusatsu Super Sentai. The characters are superheroes called "Rangers" who fight in color-coded outfits.
Contributed by Funland47
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An NPC informs the player that Gary Oak, the player's rival in the original Pokémon Red & Blue, has previously visited Kalos to study.
Contributed by blakester41
An NPC in the game questions the appearance of a Mega Pokemon, asking, "do you think all Mega Pokemon have spiky hair?" This is a reference to the Super Saiyan transformation in the Dragon Ball series.
Contributed by Dreadedpotato
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When using Surf with Lapras in the game's overworld, the player will be shown riding a Lapras rather than the black creature that appears when Surf is used with any other Pokémon.
Contributed by Fireboy
Artwork from the "Fossil Excavator" card appears in the art museum of Lumiose city.
Contributed by Cleffa
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The artwork of a Pokemon trading card, "Town Volunteers", makes an appearance in The Lumiose Museum.
Contributed by Psychospacecow
In Coumarine City there is an Ace Trainer in a house that will play a remastered version of "Unwavering Emotion", a song from Pokemon Black and White's soundtrack.
A young Professor Sycamore wrote a note to his future self, and left it in Couriway Town. It can be found and read by examining the left side of the right bench in the station there.

"To the person reading this:
What are you like now?
Did you become who you wanted to be?
For starters, what was the person you wanted to become even like?
I don't know, but it would be wonderful if you can boast that you're living each day to its fullest.
To future Sycamore.
From the Sycamore dreaming of the future."
A woman in Snowbelle City states, "Standing here reminds me of a cold region far away. Will you listen to the first song I composed there?" Answering yes will play a slowed-down version of the theme of Jubilife City, from the Sinnoh region of Pokemon: Diamond & Pearl, which slowly picks up in tempo.
Contributed by StevehPokeProf
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In Lumiose City Station, if you interact with the back of the TMV Timetable closest to the wall, it will read: 'Something is written on the back of the timetable. "I'm going to go for help. Wait in the usual place."' There is also a child standing nearby who says "It should be some place right around here, right?" People believe this child is looking for the 'usual place.'
Contributed by CodenameToast
If the player visits a Pokemon Center on their birthday, they will receive a special message wishing them a happy birthday.
Contributed by RadSpyro
On the second floor of the building to the right of the Galette stand in Luminose City, immediately after entering the floor, the lights will flicker on and off and a Hex Maniac will appear behind the player, who will then float (as she seems to lack any kind of walk animation) off screen and say, "No, you're not the one..." before disappearing.

In the first room on the right on the fourth floor of the Hotel Richissime, she will be there as well. When talking to her, she will say, "Don't talk to me... if you do, I can't hear the elevator..."

There has yet to be any explanation as to who this character is.
Contributed by tomp45673
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An NPC in the Shalour City Pokemon Center will describe a game to the player, which references another Game Freak title, HarmoKnight.
Contributed by starwindbliss
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Veteran Timeo references the E3 2007 Wii Fit demonstration by saying "my body is ready!", a phrase said during the demonstration by Nintendo of America president Reggie Fils-Aime.
Contributed by Naui
Junichi Masuda has stated that the name "Kalos" derives from the Greek word "κάλλος", meaning "beauty".
Contributed by Dazz
Pikachu's cry was changed to match how it sounds in the Pokemon anime. Pikachu's cry was also changed this way in Pokemon Yellow, and it was possible to unlock the anime call in Pokemon Stadium.
Contributed by Funland47
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A trainer in the game makes a reference to the popular "It's over 9000" Dragon Ball Z meme.
Contributed by Kodyurem
In Pokémon X and Y, Gamefreak gave a proper name to every attack that was mistranslated in the original Spanish Red and Blue versions. The changes are:

-Slam will be named Atizar instead of Portazo (Door Slam).
-Constrict will be named Constricción instead of Restricción (Restriction).
-Counter will be named Contraataque instead of Contador (Counter from the verb "to count").
-Return will be named Retribución instead of Retroceso (Return as in "Return somewhere")
Contributed by Gallego13
Pokemon X and Y are the first Pokemon games to let you select any of 7 different languages.
Contributed by WhiteSamurott
This is the first main series Pokemon game to have a worldwide same-day release, rather than releasing in Japan first.
Contributed by Funland47
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The game's region (Kalos) is based on France.
Contributed by DidYouKnowGaming
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In the 2nd UK Pokémon X and Y trailer, while Yveltal is using a Hyper Beam, you hear the sound effects for Pokemon Red & Blue's Hyper Beam.
Contributed by WhiteSamurott
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The reason Fairy type Pokemon were introduced was to balance out the game. Fairy type has an advantage over Dragon type, which was considered an overpowered type by Game Freak.
Contributed by KnowledgeBase
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In the game's reveal trailer, when the male character swings on the vines, his glasses don't follow him.
Contributed by WhiteSamurott