Latias and Latios are known as "the Lati Twins," "the Latis," or "Lati@s" when referred to collectively.
Kyogre has been called "The King of Ubers" for a long time due to being considered one of the most powerful Pokémon ever created.
Deoxys' Normal Forme is called Deoxys-N or Deo-N, Attack Forme is called Deoxys-A or Deo-A, Defense Forme is called Deoxys-D or Deo-D, and Speed Forme is called Deoxys-S or Deo-S.
Killer App: Ruby and Sapphire are the best selling titles to ever grace the Game Boy Advance, with more than 16 million units sold between them. Emerald is the third most successful with more than 6 million units sold, only beaten by the above titles and FireRed and LeafGreen.
Early on after the release of Ruby and Sapphire worldwide, rumors about being able to find wild Celebi on Route 117 cropped up, with an unbelievably low encounter rate, like one in 20 million. Nothing in the game's code suggests that Celebi can be found there. Most likely these rumors were invented by fans who were sore about not being able to trade with the Gen 2 games.
Another one involves a white rock that can be found in Mossdeep city. Apparently there is a tradition to attach slips of paper to it for good luck. This naturally spawned rumors of the rock actually being Jirachi that'll awaken when a certain number of rockets have been launched. None of these rumors are true and the white rock is just a red herring unconnected to Jirachi.
And, of course, related to the rockets was one of Gen 3's most (in)famous examples: that certain launch counts would let you go into outer space to catch Deoxys and/or Jirachi. 50 and 99 were two of the most widely-cited numbers.
It was stated in a Nintendo Power interview that Diamond and Pearl Pokémon Shellos and Gastrodon were originally designed for Ruby and Sapphire, but ultimately they were not implemented due to time constraints.
Game Freak considered altering the number of Pokémon that could be kept in the party, as well as the number of moves a Pokémon could know at a time, but eventually concluded that the changes wouldn't improve anything.
Primal Groudon is sometimes called "P-Don" or "P-Donner".
The redesigned mall-like Mauville City is sometimes called "Mallville City".
Mega Sceptile◊ is also known as the "Christmas Dragon" due to its red and green color scheme and Christmas tree-like tail.
Fandom Nod: The original games were rife with rumors that you could go to the moon on a spaceship from Mossdeep to battle Jirachi or Deoxys. Come ORAS, and Deoxys is indeed fought by riding Mega Rayquaza into space.
After Pokémon Red and Blue and Pokémon Gold and Silver got remakes during Gens III and IV, respectively, fans have been predicting that the same thing would happen to the Hoenn games. Gen V came and went with no Hoenn remakes, but Pokémon X and Y dropped several nods to the region (as well as several nods to every other region, remake or not), and on May 7, 2014, Omega Ruby and Alpha Sapphire were announced for the 3DS.
Just about everyone called Metagross getting a Mega Evolution, after it was revealed Steven had an interest in Mega Stones. Similarly, when it was revealed Maxie and Archie had Key Stones of their own, many had speculated that their signature Pokémon Camerupt and Sharpedo would receive Mega Evolutions. Come September, Mega Camerupt and Mega Sharpedo had indeed been confirmed.
With confirmation that the Hoenn Pokédex would be expanded to feature several Pokémon from Generation IV and beyond, namely evolutions of Hoenn Pokémon, practically everyone predicted that Gallade would replace Wally's Gardevoir, which was confirmed alongside Mega Gallade in September.
A lot of people suspected that Lisia was related to Wallace, due to both of them having similar color schemes and flamboyant personalities. Turns out Lisia is Wallace's niece.
Official materials state that none of the Mega Stones introduced in Omega Ruby and Alpha Sapphire can be traded over to Pokémon X and Y. In actuality, Latiasite and Latiosite can be traded and will even function since their data was left in X and Y.
The official site had advertised Megas using moves they can't legally learn, such as Diancie with Power Gem and Blaziken with Ice Punch. Once the games were out and people were able to confirm those moves were unobtainable, an official statement with an apology was released and the misleading images were removed from the site. Diancie would eventually be able learn Power Gem through legal means in Generation VII.
Name's the Same: This isn't the first Pokémon game to have a Primal Legendary. (Though this only applies to the English versions, as it was was called "Dark Dialga" in Japan)
Trolling Creator: Flygon is one of the biggest Ensemble Darkhorses from Gen III, and most people were expecting it to get a Mega. Not only does it not get one, the game's most notable Flygon user, Aarune, gives you Garchomp's Mega Stone instead.
In a Nintendo Dream interview in April 2015, Ken Sugimori revealed that Game Freak had attempted to include a Mega Evolution for Flygon in Pokémon X and Y and then Omega Ruby and Alpha Sapphire. It fell through because they couldn't come up with a design they were satisfied with.
The ability Levitate and a higher Attack boost were considered for Mega Metagross, but Tough Claws and the large boost to Speed won out due to give it more options in battle.
Game Freak trademarked "Delta Emerald" in Japan, suggesting that a remake of Pokémon Emerald may have been planned (it would have been the first "third game" to be remade). However, this may just be a blanket trademark made to cover their bases, as Game Freak has done for many other possible titles, including Grey, Purple, and Brown.