In the beginning of the series, I really wouldn’t change much, and even keep the filler. I would keep every single earning of the badges as they are, but I’d want them to be half the reason why Ash loses.
Through OS, Ash would successfully earn them, and some battles, he didn’t even train for. I’d keep that lack of training as well, and the fact that he kind of just used Squirtle, Bulbasaur, and Pikachu in battles after Charizard evolved.
Misty and Brock would constantly point this out, advising he should train with his Pokémon and get in more practice, but Ash would ignore them regardless.
When the rookie trainer loses the league, instead of just plain getting upset (which is reasonable), he would become unmotivated, before realizing that his friends were right; he needs to train more, and regains his determination with all of his Pokémon.
When he heads to the Orange Islands, he is focused on improving in his battles and with his Pokémon. He begins to connect with his Pokémon more and communicates and plays with them as well to build that stronger connection. Instead of Charizard listening to him in one episode, Ash, still along with his other Pokémon, would slowly break through to Charizard, beginning to understand and respect the fire type Pokémon, and vice versa.
To compliment this, the Orange Island gyms would hold different types of trials meant to get closer to your Pokémon, while also providing a challenge, with the Champion fight acting as a six on six battle with all the knowledge about your team gained. Ash would (like in the original) win. When he returns back home, he has his battle with Gary, which is inconclusive due to an interruption. Gary announces his plans to head to Johto, and Ash grows curious towards the new region, heading out as well.
I think all the Pokémon/evolutions/releases Ash had are fine and I would keep them the same. I believe the capture of Pokémon themselves aren’t as important as how certain Pokémon impact the trainer or their personality in general (ie: charizard, oshawott, hawlucha, some baby Pokémon).
