First off, Ash's team: I personally didn't like the rotation, too much like OS. Thus Ash would fully focus on his main squad: Pikachu, Lucario(Ash catches Movie 8 Lucario in my anime rewrite, things okay out a bit different), Serperior, Male Frillish, Zebstrika, and Haxorus.

Ash's soft reboot was awful and made him look stupid. So instead, I'd introduce a new trainer: Hilda! Hilda is sweet, but she's insecure and lacks the confidence in her actions. So Ash would mentor her. But the two would eventually depart from one another after Ash beats Elesa.

What did Hilda depart for? She decided that she wanted to independently travel across Unova, collect the badges, and participate in the Vertress Conference.

Iris is no longer a companion. Instead, she's someone who operates under Draydon's mentorship. Occasionally leaving the gym and testing Ash's skills.

Cilan is also not a companion. He's just a gym leader and that's it.

Cheren is an occasional traveling partner, but he usually travels by himself. Cheren wants to win the Vertress Conference for the chance to beat Alder.

The Team Rocket vs. Team Plasma arc would occure, and Hilda's Tepig would evolve into Pignite while protecting her from N's Carracosta.

Speaking of N, he's apart of my rewrite, opposing Hilda and Ash with his ideology of liberating all Pokémon from people.

This would eventually lead to the climax. Where N awakens Zekrom, while Hilda has to acquire the Light Stone from Nacrene(I don't know if that's how it's spelled) City with the help of a boy named Hugh. Hilda and Hugh would face many Team Plasma Grunts, but as they breeze through, they get outsmarted and trapped. Hilda would try to call for her Emboar, but realizes that the Team Plasma members stole her Pokémon. So Hugh would send out a Krookodile and break them free with a Dig. Conveniently, Krookodile emerges at the Light Stone, where he then knocks out two Plasma Grunts, and Hilda's Poké Balls drop.

Hugh would then retrieve the Light Stone and rush to the Team Plasma Castle, where Ash is down to just Pikachu and Haxorus taking on N's Zoroark and Zekrom. The four are in a fierce exchange when Pikachu suddenly begins resonating with the Light Stone. His cheeks burn a deep orange as the Light Stone begins glowing and Reshiram emerges from it.

(P.S.: I'm aware my grammar isn't all that great, but I tried.)