If I were in charge of the animé, I would have had Serena be a Sky Trainer like her manga counterpart and create a competition for Sky Trainers, where she would have to win five Sky Battle competitions, each one giving her a badge or a stamp of some sort, to become a Sky Ace. Then, there would be a final competition where all the Sky Aces would battle to become a Sky Marshal. She would eventually win the competition and become a Sky Marshal after a series of long and difficult battles. After the competition, Serena would wonder what she wants to do since she had originally wanted to become a Sky Trainer just to go against her mother's wishes for her to be a Rhyhorn racer, but even though she loves Sky Battles now, there aren't any further competitions for her to participate in.As for Ash, Serena's victory would drive him to train that much harder for the Kalos League, with Ash eventually deciding to mix and match all of his Pokémon, both from Kalos and from back in Kanto, to have him battle in the Kalos League, which he would win, with the final battle being between Alain's Mega Charizard X vs. Ash's Mega Charizard Y, with Ash's Charizard barely winning, and Ash winning the Kalos League. After that, I would have the Team Flare arc occur in a very similar way to how it happened in the animé, but I would also involve Looker and Emma and Serena would have a bigger role and battle directly in the conflict as well. The aftermath of the battle, plus her meeting with Looker, would convince her to help him and Emma start the Looker Detective Bureau.
As for Serena's crush on Ash, even though I'm no shipper, it would still be there, but Ash would eventually begin to take second looks at her, especially after she participates in the Sky Battle competitions and teaches him about them, while Ash will also teach her about other types of Pokémon battles, since she'll have more than just Flying-type Pokémon. She would have a Fletchling as her first Pokémon, which would evolve into a Talonflame, with her Kalos Starter being Fennekin, with her evolving into Delphox, with Delphox participating in Sky Battles by using Psychic to float and ride her stick. She would also get a Charmander, eventually evolving it into Charizard, which would become a Mega Charizard X, a reflection of Ash's Mega Charizard Y. This would cause her to have trouble against Trainers that used Ground and/or Rock-type Pokémon, particularly the Rhyhorn line. Her skills would also cause her to be scouted by Team Flare, which she would reject.
As for companions, if Showcases were mandate from above, I would have Shauna be a companion and have her participate in them. If that happened, I would still have Clemont and Bonnie travel with Ash and friends until he reclaims his gym from Clembot and Ash wins his badge. If Showcases were not needed, I would simply have Clemont and Bonnie still travel with Ash and Serena throughout the rest of the series.
At the end, after Serena throws Ash a birthday party where it is stated he is turning 13, I would have Ash return to Kanto with Serena staying to set up the Looker Detective Bureau, but she would tell him that there would almost certainly be branches opened in other parts of the world, so she would definitely see him again. Before he leaves, though, she would still give him a kiss, which would be shown. Ash to smile and thank her for everything and wish her luck in her endeavors, which she returns. Before he leaves, though, she would give him a holocaster and give him her number so they could talk in the future, which they would. The final scene would be him returning home with him placing the trophy in his room, along with two pictures, one of the Kalos Quartet, and another of just him and Serena, holding their trophies from their victories.
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