Note, this is a fanfic posted as a leak on this Reddit thread.
Here I will discuss a theme that many Pokémon fans will be attached to.
Pokémon Black and White were loved as much as hated when they came out in 2011. The fifth generation was brave not only because it made only new Pokémon catchable in the beginning, but even because it flipper over all tge narrative cliches of the older games: the final boss wasn't the champion, the Legendary was supposed to be caught in an odd moment of the story, the villains had apparently some justificable motivations, but, most importantly, it had a calm rival that was revealed to be the main antagonist. All of this generated these hopes and expectations in older fans: by now, every future game will have at least this depth in the plot, because the autors know that the audience got as old as the series. But with X and Y that came out in 2013, all of this got shattered: there was no narrative twist, so the events went like the games before Black and White, the characters were bidimentional and underdeveloped, the antagonists had ambiguous motivations and key points of the lore such as AZ are even now unspoken about. This was a step back, not forward, compared to the fifth generation and clearly, many were disappointed.
According to a leak made by a leaker named XYsider, X and Y were made in a really short time, this has brought to cutting huge portions of the story. These titles were supposed to have a plot that had paranormal and fantasy elements mixed: X and Y would have been about actual aliens.
The antagonists would have obviously have been still the Team Flare, but not like in the final games: instead of being some fanatics of the beauty standard for which they planned a genocide, they would have been antropomorphic aliens with the goal of destroying the planet because they deemed the warring human race unworthy of living. Their design would have been a caricature of the Men In Black. The term "Flare" is very connected to aliens: flares are flying machines used by the military to deactivate missles' sensors. They have often been mistaken for UFOs. See Phoenix's sightning for this. UFOs are hidden just like Team Flare disguised as a group of humans. The "flare" is even the planes' landing (literally, Team Landing).
Their leader, Lysandre, had a big secret: him and Professor Sycamore would have been, keep reading, the same character. They would have still had their own designs like the ones we know, but the professor would have been close to an object from space for too much time, so his DNA would have mutated. It's unclear if Lysandre was just his other form or he was the leader that possessed him, but the second one, logistically, is much more probable. In the beginning, we see two characters that are nothing other than Sycamore (earlier) and Lysandre (later). Originally, that scene would have had the purpose of making the player think about the two characters' bond. It would have been an original and innovative choice: this time, the professor would have betrayed you, even if he was just possessed. Think about it like Megaevolution, but for humans if you don't get it. Many actual Pokémon Megaevolutions would have looked like Deoxis, the alien DNA Pokémon. X and Y would have revealed the planet by which it came from: the same as Team Flare's.
What about AZ? He still stays the most obscure point in the sixth generation's plotline.
He would have been the first alien from Team Flare's species to land on the planet. He wanted to destroy it at first, but then he met Floette (it was supposed to be a Fairy/Grass Type with no evolution), bonded with her and changing his mind. He would have stayed with her until her life was over. These aliens were capable of living more than 1000 years. Team Flare would not have agreed with him and 3000 years later they would have returned to find AZ, who would have stayed on the planet, steal his key and activate the Ultimate Weapon. The mess below Geosenge Town? No, but Floette's red and black flower that he would have given to her in sign of trust. This would explain why there is no context to it in the final game. The proof of this is even that this Pokémon was datamined a little before X and Y came out with a Fairy Type move called "Light Of Ruin". This move was removed probably because it had connections with a plot section that no longer exists, when Floette had no preevolutions nor evolutions.
Other than Team Flare, there would have been even other aliens on the planet. They were supposed to be winged, dark eyed humanoids that came from the Moon. They would have been peaceful. Their leader would have been Diantha ( think about it: Diana + Anthea), but with Valerié's design. Most Fairy Type Pokémon would have been from here. On the Moon, various Pokémon would have been humanoid, just like many Fairy Type Pokémon, such as Clefairy and Gardevoir. Maybe, other NPCs like Valerié were removed just like Light of Ruin.
Gym Leaders would have all been sportives, except for Viola, that would have been Ghost Type and with a passion for UFO photos. Ironically, her sister would have been kidnapped by Team Flare.
What abour Xerneas and Yveltal? Would they have been energy sources for Floette's flower? No, they would have been godlike alien weapons that AZ would have brought with him to ensure the total erasure of life from the planet depending from the version. This would explain why Zygarde is supposed to be the protector of the ecosystem: the god would have perceived the alien threats and fought them. Zygarde's cells would have served as spy cameras. The fact that Xerneas and Yveltal were so powerful would have even made sense for Zygarde's forms to be based on Loki' s offspring: 10% = Fenrir: when Ragnarok will come, his chain will break.
50% = Jormungandr: when the giant serpent will bite his tail, succeding in circling the world, Ragnarok will come.
100% = Hel: the Maiden with a skull half on the face who rules the Dead's realm. When Ragnarok comes, the Dead's souls will fight.
We never got Pokémon Z because it required a lore and story sections that no longer exist.
THIS is what Pokémon should be. I would wait even 3 or 4 years for something this good!