Ash: I want to go back to the day my journey began, when I first set off from Pallet.
Sir Aaron: Hah! Told you, you great lump.
Arceus: I thought 'any day but then' was good odds.
Ash: Were you two betting on me or something?
Sir Aaron: Err… nooo?
Ash: Somehow I don't believe you.
Arceus: Now, Dialga!
Narration: In that second of absolute stillness, Ash thought to himself that using the – a – legendary Pokémon that controlled time to get out of an embarrassing situation really took some beating. Then there was a roar, and he fell into blackness.
—This is how readers know that they are guaranteed a great fanfic in the humor genre that's gonna have them die laughing.
Most notable in the case of Ash's Charizard when using Blast Burn. For context, in the games, Frenzy Plant, Hydro Cannon, and Blast Burn are the Grass, Water, and Fire (respectively) versions of Hyper Beam. In this fic, when Ash's Ivysaur and Squirtle use Frenzy Plant and Hydro Cannon, that's how they're portrayed: as powerful but draining finishing attacks. In contrast, Charizard's Blast Burn is equivalent to a tactical nuke.
Battle in the Center of the Mind: Used twice so far via Aura Purge. The first time was to help cure Misty's phobia of Bug types by going back to her memory of the traumatic event that caused it and battling a horde of Bugs led by a mental projection of Genesect. That fight was used as a practice run for the battle against Sabrina, which culminated in the only sane fragment of her personality cutting down her inner darkness with a representation of Keldeo's Sacred Sword, Excalibur Galatine.
Berserk Button: For Pidgeot, being mistaken for a male. The first time it happened, she retaliated with a massive Sky Attack and left the message "I'm female, twit" carved into the surface of the glass lining the resulting crater. Subverted the second time, when the culprit managed to apologize for his mistake in time to prevent her wrath.
Curb-Stomp Battle: Due to Ash being able to restore the memories, and power, and evolutionary level, of his Pokémon, and that of his friends, including Jessie, James and Meowth to whatever they were before Cyrus did his thing, they meet some people who they completely overpower.
Early on, when Ash encountered the samurai guy who uses Bug-type Pokémon a second time from his point of view, well, it is easy to guess how that went.
When they did the Princess Tournament again, the early rounds, in the author's words, were one-sided.
Discontinuity Nod: Dexter brings up the events of the infamous banned Porygon episode, which none of the others can remember. He attributes the memory loss to epileptic attacks brought on by the digital environment.
Evil Versus Oblivion: The purpose of Rocket executives, or at least the department the promoted Jessie, James, and Meowth are in. You can't rule or make a profit in a destroyed world, so somebody needs to point Idiot Heroes in the right direction to protect all those potential victims.
Field of Bones: Jessie's Cubone (based on Archer) can manifest her reality marble, which takes this form.
Fix Fic: Technically a subversion. Most Fix Fics completely ignore canon after a certain point, but this one only works because the characters have knowledge of canon.
Friendly Enemy: Jessie, James and Meowth. After their memories got restored and Ash explained the situation to them, of course.
Hopeless Boss Fight: Ash's Gym Battle against Misty was supposed to be this in order to teach him humility, since in this fic, Gyms are designed to test a Trainer's character as well as their battling prowess. Unfortunately, Ash didn't get the message and ended up accidentally bringing the roof down as a result of his refusal to give up.
Instant A.I., Just Add Water: Dexter, as well as Gary and Professor Oak's Pokedexes, develop full sentience as a result of uploading all the information Dexter had catalogued from the future and become Porygons.
King of All Cosmos: Arceus and the second Dialga and Palkia, much to Sir Aaron's dismay. "Every hour I'm in here with you guys, my image of the Kami becomes a little more tarnished..."
Lampshade Hanging: Some of the sillier/weirder/crazier stuff that happened in the anime gets commented on by the characters.
Large Ham: Ash's Squirtle, oh so very much. Same with Gary's Blastoise. Ash has this to say about his Squirtle:
Ash: I've heard of showy, but that turtle takes the cake.
Mewtwo lampshaded it asking if Gary's Blastoise was feeling well.
Meanwhile, in the Future: The story frequently cuts to the sub-dimensional bubble where Arceus, Sir Aaron, Dialga, and Palkia play lots and lots of board games while waiting for Ash's changes to the timeline to take effect.
Mid-Battle Tea Break: A literal one happens during Ash's gym battle against Erica. Ivysaur and Gloom are locked in a stalemate against each other, easily healing any Scratch Damage the other manages to inflict. During that time, Erica and Misty enjoy a Spot of Tea, a bored Ash starts looking up the record for the longest Pokemon match in history, and both Pokemon resort to using the nearest computer to look up their movesets in search of anything that will turn the tide one way or another.
Mission from God: Arceus himself gave Ash the mission of making sure Cyrus doesn't succeed.
Mythology Gag: Arceus creates a second Dialga to send Ash into the past, and later creates a second Palkia to round out his gaming group. In Heart Gold and Soul Silver, Arceus could create a copy of one of the Sinnoh Dragons if brought to the Sinjoh Ruins.
Ash mentions having Dexter develop a way to jailbreak TMs so they could be used more than once while they were in Unova during the original timeline.
James expresses surprise at not whiting out and waking up at the Pokemon Center after running out of usable Pokemon during a battle.
Ash and Gary face each other in the finals of the Indigo League.
Nice Hat: Sir Aaron's hat, which grants its wearer the Dark subtype.
Secret Test of Character: Giovanni orders James to give up his beloved Growlie so the Team Rocket highers-up could use his firepower. James ultimately refuses, with Jessie and Meowth backing him up. This convinces Giovanni that the trio have what it takes to be promoted to Executive status and learn about Team Rocket's secondary goal (see Evil Versus Oblivion above).
Ash goes to Cameran to free Aaron's Lucario and collect Aaron's equipment right after getting the Boulder Badge. Compare to the original timeline where he only went to Cameran after the Hoenn League during the Battle Frontier arc.
Ash clashes with Hunter J before he finishes the Kanto League, about the time he was supposed to get Muk. In the original timeline, Ash clashed with Hunter J while in Sinnoh.
Ash captures Muk way later than the original timeline, while helping that movie director, because he forgot about Muk due to the battle with Hunter J.
Stating the Simple Solution: Some characters point out to other characters very simple solutions to problems they had during the original timeline. Vague wording due to the fact that the relevant positions are sometimes switched around.
Super Empowering: Ho-Oh grants Togekiss the ability to use Sacred Fire as a birthday gift.
A Running Gag throughout the fic is how just being around Ash seems to trigger evolution in other people's Pokemon, even the ones he can't restore to the way they were at the end of the former timeline.
Weather Dissonance: The crazy weather Ash and the others have to put up with on occasion is implied to be a result of Butterfree disrupting the weather patterns when he used Sunny Day in the middle of a rainstorm to save Charmander's life. Another possibility that gets suggested is that temperamental Legendaries are to blame.
You're Insane!: Aaron's reaction to the concept of a "Legendary Pokemon Three Legged Race," especially since there are so many variations on how pokemon move- ranging from hovering (no legs) to having too many legs for the race to work. Arceus admits that the whole idea was because he was running out of games.