Why did the reaction of Absol turn from the fan-perceived 'stalked by Absols' to being actually Nightmare Fuel for them? It is the job of Absol to warn of disasters, and appear to humans to warn them that a disaster is near. They do not seek them out.
Ash losing to Casey seems like just a random FEAR joke, but it actually references how Ash starts many new regions by losing a battle he should have won.
To qualify for the post of gym leader you must face the Elite 4 Challenge with rented Pokemon, and give a good showing. Is it any strange that Giovanni, who was a legitimate gym leader, is such a badass?
Ash is pretty much doing a New Game Plus. This also explains why he didn't go off to fight Team Galactic immediately: Cyrus is the Bonus Boss and Ash and co. have to Level Grind.
Why are there multiple Reshirams and Zekroms? Because there are multiple of each in both the anime and the games.
There's one of each in Unova and Hoenn each in the games, and there's two pairs minimum in the anime - one pair from the movie, and at least one pair from the anime, which can't be the same because a Zekrom attacks Pikachu in the very first Best Wishes episode.note To wit, if the movies are considered Canon (Saphroneth does) then there has to be at least two- Depending on the version of the movie, either a Reshiram or Zekrom has been sealed in Eindoak Castle for a thousand years. If there was only one pair, then Zekrom being sealed meant that Ash could never have met the one that blasted Pikachu at the start of Best Wishes- but Reshiram being sealed meant that N could never have met the one in his childhood. Plus, Hoopa summoned both of them in the backstory of his movie, and that was less than a thousand years ago.
Jokes aside, it very much makes sense for the Illusion Gym Leader to pretend to instead be a Rock Gym Leader. After all, every gym carries a lesson related to its focus, and Brock just wouldn't be the Illusion Gym Leader if he didn't insist that he isn't.
It makes sense that Mastermind of Mirage Pokémon would be on Ash's birthday, since the canon version was originally an anniversary special.
The Dark City gyms truly embrace the nature of its chosen type. Dark-types are known for utilizing misdirection, are ruthless in their tactics, and bend, if not outright break the rules. The first thing the gym does is lie about its own nature. They use many Pokemon that are not Dark-type, pointing out the loophole stating they don't HAVE to use their nominal type, just be proficient in it. And when a trainer finally wins and thinks they're in the clear, the other gym leader is preparing to fight them.
Apparently the gym as a whole does not have to have a singular type, but each gym leader does. This explains how Cilan and his brothers are able to run their gym despite all three of them not focusing on the same type.
Ever heard the idea that the Fairy-type was developed by a little girl who likes cute things and has the strength to beat down the big scary dragons and big scary men? Well in this fic, the first Fairy-type around was Sylveon, dreamed up as an evolution to Eevee by Molly Hale, and when she became real, a Time Crash allowed Arceus to use her typing as the basis of all Fairy-types.
Rayquaza has been assigned the secondary duty of stopping incoming meteorites ever since Arceus got hit with the one that killed the dinosaurs. Rayquaza said that Arceus was fine because he had all his plates, but was reliably told that it hurt. Rock is the only type that is super effective against more types than it's not very effective against and no type is immune to, so it would be the best type to use against a theoretical "every-Type" Pokémon.
The God Squad coming out of the GS ball in the Battle Finale of Legend seems like a poorly thought out Deus ex Machina at first. However, even if you ignore the Assist-induced Judgement, which is already a giant hint, there is one more hint that was planted hundreds of chapters earlier in advance which gives away the fact that the GS ball is a doorway to Arceus' realm, the fortress of Gold and Silver. GS also could easily stand for God Squad and in the original canon, Gold and Silver was what the GS ball was called. Not only that, the GS ball is completely unscathed after being hit by Roar of Time, which shouldn't be possible unless it also exists on a cosmic tier. The hints were right in front of us the whole time!!
Every time you laughed at Brock's reaction to hearing Professor Ivy's name or Misty's fear of bug Pokémon, you're laughing at the most traumatizing moments of their lives.
Notably, while Professor Ivy's original fate isn't canon, it does successfully explain away why Brock would throw away his one chance at love, especially since Brock's scenes up until then show he's largely happy at her lab.
Ash can only restore the memories of the people and Pokemon he knew well... so what happens to the millions from the original timeline whose lives are irrevocably changed now?
It's their new normal; unless they're someone that someone restored by Ash or Ash himself told about the original timeline (like Charla, Professor Ivy or Norman), they're not going to know there was ever a difference.
It's been shown that Goodra and Mawile are really good friends. Pokemon Sun's Pokedex reveals that Sliggoos have trouble differentiating the difference between friends and food and may even try to EAT those they get along with. It's probably a VERY good thing that Mawile had him evolve so quickly.
Mind you, the Pokedex is often filled with hyperbole and outright misinformation (saying certain pokemon are incapable of being trained yet the anime shows them as being trained or friendly, or showing apocalyptic consequences for Pokemon doing normal things), so it's unlikely that this would have come to pass.