Ascended Fanon / Throw It In: For a long time people have been asking Game Freak to change up the starter trio instead of always doing Grass<Fire<Water. The most common suggestion on how to do it? Fighting<Psychic<Dark. Gen 6's starters in their final stages are Grass/Fighting < Fire/Psychic < Water/Dark.
The fact you have to hold the 3DS upside down to evolve Inkay may be a reference to the old April Fools joke of evolving Lickitung into Luigi by holding your Game Boy upside down. Since the fine folks at Nintendo themselves started the rumor, it's most likely intentional.
Chespin's first evolution Quilladin is often nicknamed Chespińata, due to its round, bloated shape.
Froakie is being nicknamed Benjamin Froaklin for his resemblance to the Founding Father. Also, some who hope for a dark-psychic-fighting reverse circle call it Hypnotoad.
Kyubey is a popular nickname for the new eeveelution, Sylveon.
DRAGON SLAYER for the Fairy types.
Hexcalibur for Honedge.
"Mewthree" (harkening back to old Gen I rumors) for Mewtwo's Y Mega Evolution, before it was revealed as a forme rather than a new species. "Newtwo" is also common. Also, due to its similar appearance to Buu, it has been nicknamed Mewbuu and Mewjin Buu.
Ampharos' Mega Evolution has given it the names Amphabulous and Amphabio for its long, flowing hair.
Many also guessed Pancham would evolve into Fighting/Dark and lo-and-behold, they were right.
When Sylveon was revealed, some guessed that it would be a brand new type. They were right.
Many fans speculated that Mawile would gain Fairy-type, and they were right. Bonus points for being the first Fairy that can really be described as The Fair Folk (as in "A fairy that's evil and/or mischievous, not one that's bright, pretty, and kind-hearted"), which was a popular theory for the type.
The most commonly guessed weaknesses for Fairy were Poison and Steel, often going off a highly-accurate leak that claimed this. Both were revealed to be the Fairy-type's only weaknesses.
After the initial batch of Mega Evolutions was revealed, the Kanto starters were among the most common picks when guessing who would get one next. Sure enough, this was proven right.
People have been wondering and debating over why Charizard is not part Dragon-type, possibly since Generation II. Finally, their prayers have been answered with the reveal of Mega Charizard X, a Fire-Dragon type.
The same could be said about Ampharos, which was not a Dragon type despite its Japanese name being Denryuu ("thunder dragon") and knowing Outrage since Gen 4. Come Gen 6, we get Mega Ampharos, Electric/Dragon.
This deviantART user made a Fan Pokemon called "Noibat" which emphasized on its ears. Guess what Noivern's pre-evolution is?
In the original reveal trailer people noticed a girl following Calem in the forest. There was debate whether it was an important NPC (probably a rival) or a character with a pre-made course, like a biker in previous titles, because they weren't exactly behind Calem and their design was deemed too generic. Come a few months later and that's one of your rivals, Shauna.
When promotional artwork of Sylveon was shown fighting Hydreigon, several estimated the possibility that Hydreigon would have a quadruple Fairy-type weakness. A few months later, the charts come out and confirm this due to Fairy being super-effective on both Dragon- and Dark-types.note Incidentally, Sylveon is one of the few things that essentially hard-counters Hydreigon, even those with Flash Cannon depending on the build.
Some fan prediction artworks of Mega Medicham featured four arms. The real one has manifested four additional ribbonlike arms with its psychic powers, in addition to the two it doesn't use.
The Fighting/Psychic/Dark starter trio that have been speculated since Gen II have finally come into fruition, though ironically as secondary types of the traditional Grass/Fire/Water typing.
Many fans speculated Diancie to be related to Carbink due to its Rock/Fairy typing and similar looks. When Diancie was officially revealed, it turned out to be a "sudden transformation" of Carbink.
Schedule Slip: Pokémon Bank had to have its international release postponed after its release in Japan coincided with the massive influx of new Christmas users for both the 3DS and Wii U and implementation of new user profiles for old accounts, causing Nintendo's online services to screech to a halt.
Screwed by the Lawyers: X and Y was released early in Italy and Canada which resulted in leaks that caused Nintendo to crack down hard on the leakers and the stores that broke street date on the games.
Tipping NPC's with the max value of 1,000 all the time increases the chance of Shiny Pokémon appearing. Allegedly.
Sundry rumoured moves on Pokémon, such as Froakie getting Rapid Spin by egg.note It doesn't. Being unable to data-mine 3DS games doesn't help with this situation.
Given that new Eeveelution's have always released in pairs, and Nintendo has been known for not advertising Eeveelution's in the past (Glaceon and Leafeon weren't known until hackers saw their sprites in rips and thought they looked a lot like Eevee), there are rumors that there's a secret second Eeveelution in the title.
There were also rumours on how the latest Pokemon evolves. For example, it was thought Honedge needs to defeat another Honedge to evolve (probably to gain a new sword), and Clauncher and Skrelp evolve by levelling-up while knowing Crabhammer and Camouflage respectively.
Although the games can't be data-mined yet, people have found what appear to be three event legendaries: Volcanion, Hoopa, and Diancie. First their names showed up as GTS requests, then alleged pictures were posted by a hackernote The game-cartridges themselves can't be hacked, but these pictures were allegedly revealed by memory-hacking. The same hacker revealed the 3D model of AZ's Floette, but only Diancie is confirmed to be real. The names are though, as only real names are accepted by the GTS.