Alternative Character Interpretation: Quite a lot. As the Pokémon usually do not talk, and a number of them never really established a gender, interpretation can run pretty wild here. Usually Played for Laughs though.
One of the most notable in the series is Squirtle being a Kamina Expy, considering that Squirtle predates Tengen Toppa Gurren Lagann by about a decade (and had Kamina's sunglasses first).
While not that much of a Base Breaker and more of fandom dissonance, the fans reaction to the Oogakari Pokémon cameo is split between those who enjoyed Yet again, with a little extra help and loved the cameo, those who felt the inclusion of those characters made it seem like a badly written omake, and those who simply loved the battle and didn't care much for the characters (mainly because they had never heard of Yet Again).
A number of fans dislike how Whitney was made into a butt monkey. Others really liked it, see the below Take That, Scrappy! entry.
Ash's Legendary Maid Service for Mewtwo. Considering he tends to keep situations like the one at Shamouti from going completely out of control on his own, it's a nickname that is well deserved.
Wallace's supercharged Magikarp is nicknamed Hyperkarp.
Arceus and the new Creation Trio are collectively called the God Squad.
Deoxys from the Delta Episode is nicknamed Deoxys Bad Driver.
Growing the Beard: Many agree the series quality went up following the hiatus period before Movie 2. In fact, in March 2023, Saph updated the first 42 chapters so they'd be on par with the rest of the chapters.
Heartwarming in Hindsight: The fic has Ash reuniting with his Pidgeot and Butterfree and Journeys would later have Ash reuniting with both of them in canon as well. In addition, Pidgeot rejoins Ash's team permanently just like Pidgeot does here.
Since the fic was started before Generation VI, it originally lacked Fairy-types and Mega Evolution, and the author Retconned those elements into the story with a Time Crash, making it so that they always existed. Afterwards, The Game Theorists made a video, "The Pokémon Multiverse Explains Everything", which postulates that the games with Mega Evolution are actually in a different universe than the ones without it. That then became its own example when Omega Ruby & Alpha Sapphire had Zinna imply this to be the case, and then for Sun & Moon to outright confirm it with Anabel and her team being refugees from said other universe.
The sudden influx of years of data causes Dexter to upgrade into a Porygon, able to, among other things, translate for humans that can't understand Pokémon. Cue the introduction of the Rotom Dex in Pokémon Sun and Moon.
Even better, the possibility of a Rotom possessing a Pokédex was brought up in Chapter 151, about six months before the reveal trailer.
Even better, Pokémon Masters gives us a form of Porygon-based Pokédex in the Poryphone, an analogous of sorts to the Rotom Phone introduced as a replacement for the Pokédex in Pokémon Sword and Shield.
Alolan Raichu are part Psychic type. Sound familiar, Sparky?
With the concept of Z-Moves, along with Gigavolt Havoc being heavily associated with Pikachu in particular, it's funny to think that Volt Crash, in a sense, is now canon.
And it goes even further than that! Ash and Pikachu invent a powerful, never-before-seen electric move. Here, it's Volt Crash. In canon, it's their one-of-a-kind Z-Move, 10,000,000 Volt Thunderbolt.
It happens again in Pokémon Sword and Shield, where Gigantamax Pikachu's special G-Max move is named Volt Crash.
More minor, but the character Simon from Johto who can understand Pokemon explains that he doesn't understand exactly what they say, but can sense what they mean. Several months later, Ash's gym battle with Valerie aired, and he gives the exact same explanation for how well he understands his Pokemon.
And both characters are Aura adepts in Ashes. How about that...
Brock and Misty's usage of Mega Stones for Steelix and Gyarados, respectively, in fic becomes this with their return in Pokémon the Series: Sun & Moon, in which the two do in fact Mega Evolve.
Ash getting strong enough to seriously fight the Elite Four and Champion on equal footing. At the time the story started, this seemed an impossibility in canon, thanks to his portrayal in Unova. Then Kalos and Alola came along, and this fic's portrayal of Ash's competence suddenly wasn't that far off. And then Galar happened and his portrayal there rivals or even exceeds what is shown here, which is no small feat.
In this fic, Ash catches Keldeo, a Mythical Pokémon, as a temporary team member. This, again, is something that seemed absolutely impossible in canon... Until Ash catches Meltan, a Mythical Pokémon, as part of his team for Sun and Moon and it doesn't ends released at the end, instead staying with Ash's Alolan family along with Ash's other Alolan mons.
Ash winning a Pokemon League was a big deal when it was done here. After he did it in the real show, his win here isn't as important in retrospect.
Team Rocket having a significant interaction with a Cubone. In Ashes, they took one in in an early chapter around Lavender Town. Then, years later, along comes Pokémon Let's Go, Pikachu! and Eevee!, where Jessie and James capture a Cubone in Lavender Town (although not as positively).
Ash getting a Riolu by hatching its egg with his aura. Here, he's reminding the Riolu he met in Sinnoh, which causes him to hatch immediately. In canon, Riolu senses Ash's aura while still in its egg, and quickly hatches after Nurse Joy entrusts the egg to Ash after seeing it react to him.
Throughout the story, Ash has come into ownership of multiple legendary Pokémon, though he lets them go off to do their duties while still having their Pokéball to call on them for emergencies. Come Journeys Episode 53, and Goh has now found himself in the same situation with having caught a legendary, but letting them roam free. Bonus points for Goh’s catch being a Suicune, which is one of the legends on Ash’s team.
In Ashes, Riolu evolves due to blocking an attack by Hunter J. In Journeys, Ash's Riolu evolves due to blocking an attack by Chairman Rose.
In this fic, Ash uses Sir Aaron's staff, with the Rainbow Wing and Silver Wing attached to it, as a makeshift keystone and can mega-evolve his Lucario. Come Journeys Episode 84, Ash now has both a keystone and Lucarionite to mega-evolve his Lucario.
After winning the Sinnoh League and defeating the Elite 4 as of Chapter 305, Ash is slated to face Cynthia. Around a year later, Journeys has him being among the Masters Eight, where his second fight is against Cynthia. Both scenarios also take place after Ash actually gets his respect. Saving the universe in here and being a league champion in the anime. Taken even further later down the line where the anime outclasses the fic by having Ash win the tournament itself and become the World Champion.
Pikachu's "Zappy" ability allows him to bypass type-based immunity. Pokémon Mystery Dungeon: Rescue Team DX reveals the rare quality Steamroll, which allows the player's team to bypass type immunity, meaning that electric types can finally electrocute Ground and Rock types.
Shocking Moments: The appearance of the original timeline's Team Galactic caught many people by surprise.
Take That, Scrappy!: Whitney's Miltank is quite hated by those who played the second generation games and their remakes due to how difficult it is to defeat. Then, in his gym battle with Whitney, Ash humiliates it when his Muk fires Thunderbolt, Flamethrower, Shadow Ball, Rock Tomb, Shock Wave, Fire Blast, Focus Blast, Secret Power, Dark Pulse, Sludge Bomb, Giga Drain, Hyper Beam, Ice Punch, Hidden Power, Double Team, Round, Payback, Rain Dance, Sunny Day and Toxic at the same time, and later Raikou inflicts it a One-Hit KO with a creative use of Nuzzle... That is, the weakest damage-dealing Electric-type move. Though it is a Legendary using it, so "Weak" is still probably more than most 'mons can handle.
One at the very beginning: when Ash had a Riolu egg delivered to him, he never expected it to be the Riolu he had saved from Hunter J all the way in Sinnoh in the original timeline.
In the episode "The Little Big Horn", Brock helps a wild baby Stantler. The fanfic's adaptation has that Stantler join Brock due to the different circumstances (no Team Rocket, Togekiss consoling the Stantler, etc). He is just the first of several Pokémon of the Daythat join the main cast.
Another one shows up in the Silver Conference where the bug samurai that Ash curb-stomped in Viridian Forest shows up as one of Ash's opponents and he shows Ash just how much he's improved...
If you thought the bug samurai was already an unexpected character, he merely pales in comparison to Steve (Third Fang) and his roster who are Pokémonified Oogakari!
James has a Moltres now. What.
The trade between Ash and Gary results in Ash getting the Goomy he met in the XY anime, but whom he never encountered in this timeline.
May's Glaceon shows up in mid-Hoenn as the egg of Drew's Leafeon.
Of all the Pokémon that could join TR's cell, impressed with her Contest skill, Wallace gifts Jessie a Pikachu. But not just any Pikachu; she's a cosplayer!
Just after the Battle Factory, Lugia shows up with Manaphy's egg.
Dawn's Buneary shows up when Ash and the gang are in the Battle Frontier. And then her Pachirisu follows soon after. And then all the rest of them.
Philena eventually catches a Rockruff for Brock. It then turns out to be a Zorua in disguise. Though Brock does get an actual Rockruff later.
The titular Giratina from Giratina and the Sky Warrior being reminded and joining Ash. What makes it unexpected is that the capture of the Lake trio beforehand has rendered Ash being unable to Remind people of the previous timeline.
about six months before the reveal trailer.