XY are a trilogy.
Pokémon X and Y's plot in a nutshell is you and your four friends touring around Kalos to discover the secrets of Mega Evolution. Along the way, you all fight off Lysandre to stop his plans of mass genocide, then by the end of the game, you inspire AZ to finalize his path of redemption. During XY, Lysandre worked with a group of five scientists to locate the legendary Pokémon (Xerneas/Yveltal) who could be utilized as a greater source of "infinity" energy for the Ultimate Weapon than what AZ used 3000 years prior. Xerneas and Yveltal have a third legendary who accompany them, called Zygarde, but it only arrives when Xerneas and Yveltal are in real danger or if the natural order is being disrupted in some other way. It doesn't seem as if XY did put them through enough danger because despite Lysandre draining 99% of their energy all they did was miraculously wake up, take back most of their energy, and break through the weapon as you arrived. These legendaries either create and give off life energy (Xerneas) or take and destroy life energy (Yveltal). They could not really be threatened by this and they've proven this to Lysandre even within Team Rainbow Rocket. Lysandre would not have had Xerneas/Yveltal on his team in USUM if his plans were 100% fulfilled. Even in the Kalos manga Xerneas and Yveltal prevented Zygarde from arriving to Lysandre. This left Zygarde hanging without a suitable role in all of XY's plot.
ORAS is a sequel to XY. This may sound weird and people often think ORAS took place during the same time as FRLG because RSE did for sure, but I think in the Mega Evolution universes, ORAS took place much later than RSE and around the same time as XY. To start off, Zinnia finalizes the lore on Mega Evolution and explained the cause of it was AZ's Ultimate Weapon. She also mentioned how AZ was in Sootopolis, witnessing the very first Mega Evolution happen live during a fight between Primal Kyogre and Primal Groudon. She then summons Rayquaza to have it mega evolve and have you save the world from a giant meteor. Kalos had the technology to be aware of a meteor threatening the entire world and should have known about this in XY had it taken place before then. By this logic, they should've also known of a Mega Rayquaza. Additionally XY and ORAS events happen similarly near each other in the anime, the manga utilizes the old and new team magma/aqua people as two completely different people, and nothing in Gen 6 indicates any significant time travel between XY and ORAS. We also know that LGPE does
not take place during the same time as RBY/FRLG thanks to Red and Blue being established while Team Rocket events were ongoing and Mina being about only 5 years younger when SM/USUM takes place a minimum of 10 years after RBY/FRLG. Lastly, Wally in SM/USUM looks as if he aged significantly less than Red and Blue have. It is very possible for ORAS to take place during XY in mega universes while RSE happened during FRLG in non-mega universes.
A smaller thing relates to how Alpha is the first letter of the greek alphabet and Omega is the last letter of the greek alphabet. It's sorta like "Pokémon AZ" if you know what I mean. They also had Archie and Maxie create something known as "
Project AZOTH" in ORAS, which would be a plan to bring an end to all life from Earth and reset everything to a new beginning. A grunt even confirms that "A" stands for beginning and "Z" stands for end in Project Azoth. We even have Zinnia in the game with her partner being a Whismur named Aster. A and Z respectively. Gamefreak clearly knew what they were doing here.
Another major point about ORAS is the confirmation of multiverses. Zinnia confirms that Pokémon was not just one universe, but an entire multiverse filled with (at least 2) separate universes. Archie and Maxie also vaguely hinted out that Omega Ruby and Alpha Sapphire are another two separate universes and when you reach the Battle Resort, you find Looker. He was washed up on shore and a woman brought him to her cottage, saying he fell from the sky and has amnesia for some reason... little did we know this would be the biggest foreshadowing of the next generation for its time.
SM and USUM expanded on the information ORAS gave to us to the utmost extreme by making its lore and plot mostly about Ultra Wormholes. Ultra Wormholes are portals that grant access to Ultra Space. Ultra Space is an indefinitely-expanding dimension with countless amounts of portals all leading to separate universes each. They also inhabit a large group of special Pokémon known as the Ultra Beasts. The Ultra Beasts are invasive species of Pokémon to the natural Pokémon world and their existence in Alola defies the world's natural order. This is the big thing Zygarde WOULD be largely present in a Pokémon game for. Zygarde was checking out Alola to scale how threatening the Ultra Beasts were, since they were species of Pokémon who didn't belong to the order of nature. However, there were never that many to begin with and we dealt with most of them by ourselves in the Gen 7 games. Zygarde was there but never had to go to the extreme of becoming complete. Additionally, there were people who fell from the sky out of Ultra Wormholes. The Ultra Wormholes would take them from their old universe to SM/USUM's current universe and give them amnesia. This sounds exactly like what happened to Looker in ORAS Hoenn; although the Looker in SM/USUM seems to be a different Looker altogether (yes this means there are at least two Looker roaming around in one universe). With Gen 7 giving a significant role to XY's Zygarde and heavily expanding on the event ORAS foreshadowed, I can confidently say that Gen 7 is the third installment to the XY trilogy. SM and USUM are two separate universes of their own with different plots during the same time, so USUM isn't a sequel but rather a game where events in SM took a different path.
For a couple other things, Magearna was the first Generation 7 Pokémon introduced to the series. Its lore states that it was created by a scientist 500 years ago to accompany a princess. We later learn from the release of its own movie that it was created in what was known as the
Azoth Kingdom in
Kalos; the same name as Archie/Maxie's plan in ORAS. We can also say that Magearna's creation was inspired by AZ's Ultimate Weapon. Magearna is a machine fueled by the life energy of other Pokémon. When it uses its signature attack, its hand opens up in a flower-like shape and unleashes a powerful beam. AZ's Ultimate Weapon is also a machine fueled by the life energy of other Pokémon and it also opens (something) up in a flower-like shape to unleash a powerful beam. This next part might be a big coincidence but Magearna was also the biggest overall check to the combination of Xerneas and Yveltal in Gen 7 Ubers/AG metagames and would be the biggest counter to both against Yveltal lacking Heat Wave. It resists all of Xerneas and Yveltal's STABs and fires back with Super Effective attacks against both. It even had Heart Swap to steal all the Geomancy boosts from Xerneas back then. Coincidence?
Additionally Ash Greninja was featured in SM. It took a significant role in the XY and XYZ anime before leaving Ash at the end of his Kalos adventure.
Lastly, Generation 7 just seems like an expanded iteration of Generation 6. Mega Evolution and Primal Reversion were kept in main series, Pokémon Amie was changed into something considerably close, items like the Vs. Recorder functioned mostly the same, the same 60 minute battle timer was carried across from the previous Gen 6, a plethora of older gen characters made a return, both Gens 6 and 7 were the primary games for the Pokémon Bank app, the 3D models were the
exact same(?), not even re-polished or rendered differently?, Gen 7 did not add anything super big to the series unlike Gen 6, but not remove many notable things either. There is probably a lot more but, Gens 6 and 7 feel connected to each other than any other two gens do to each other, even Gens 1 and 2 despite Gen 2 being a confirmed Gen 1 sequel. Gen 7 finishes off Kalos, expands on ORAS discoveries, and does not fundamentally change itself into a series reboot in any real way unlike most generations prior. Because of all of this, I consider all the 3DS core series games to be part of a trilogy between one another.
