Kanto: Ref of the 5th match gets taken out by the mafia (or just conveniently knocked out by TRio), allowing Ash's match with Ritchie to be a bit more dignified given how screwed over he was. Make it like the Electric Tale of Pikachu version where Ash's lack of training comes into play more obviously.
Orange Islands: Paralysis isn't fainting, either, ref. But Ash pulled through and won anyway, so it doesn't matter.
Johto: Nothing.
Hoenn: Have TRio start out rooting for Tyson because Meowth admires his Meowth, but have Pikachu vs Meowth first and Pikachu wins, so they switch back to cheering for Ash.
Sinnoh: Not only have Ash deliver an absolutely crushing, effortless defeat to Paul, but have Paul's crimes revealed to the people on national television (including to his brother, who would be horrified by his treatment of his Pokemon) and have him stripped of his right to be a Trainer and have all his Pokemon taken away from him permanently. Tobias battle remains unchanged.
Unova: Have Cameron bring 6 Pokemon, let Snivy defeat his Riolu even after it evolves, have Ash lose to Cameron's 6th Pokemon in a hard-fought battle.
Kalos: Show Ash's preliminary matches, make Pikachu the final opponent against Alain.
Alola: There's nothing to fix here except maybe extending the Battle Royal round to two episodes so we can actually see more of the takedowns.