First of all, I would make the characters a bit more mature and less whiny. I think the dialogue in the 5th and 6th gens has become so child-like. People say that it's because they're aiming for a young audience but they never seemed to speak like that in the first gens.
There are sooooo many things I would have changed about Ash's pokemon teams in each gen.
Kanto: I would have given Ash a Cubone after Butterfree was released.
I would have had him catch 30 Tauros in the Safari zone, but only keep one and release the rest back into the zone.
I would have given Snorlax, Tauros, Kingler and Muk more time on Ash's actual team rather than being Oak'd.
Johto: I would have evolved all three starters to their second stages (Bayleef, Croconaw, Quilava).
Hoenn: I would have given Ash Sableye instead of Snorunt/Glalie
Sinnoh: I would have given him Gligar earlier on so it had more screen time before evolving. They evolved it very quickly.
I would have evolved Gible into Gabite.
I would have had Ash catch Buizel from the start, not Dawn.
Ash kept Aipom but it never evolved (Didn't like Ambipom)
Unova: No rotating team.
Would not have given him Snivy as his rival had it and he had Leavanny.
I would have given Cilan Snivy as he's meant to be a grass trainer and it just suits him more.
Would have give Leavanny more development.
Wouldn't have evolved Krokorok into Krookodile. Also get rid of the cheesy glasses.
Never would have given him Unfeazant. It's boring and ugly.
Would have made Ash catch a Rufflet and evolve it into Braviary.
Wouldn't have given him Palpitoad either. Ended up being irrelevant.
Would have made Scraggy get stronger so it's actually usable in battles, but not evolve.
His final Unova team would have been Pikachu, Pignite, Boldore, Krokorok, Leavanny, Braviary, Oshawatt and Scraggy.
Overall: By this point going into 6th gen all the pokemon he has at oak's (or elsewhere) would be;
Pikachu, Charizard, Snorlax, Kingler, Muk, Tauros, Bulbasaur, Squirtle, Cubone, Bayleef, Croconaw, Quilava, Heracross, Noctowl, Sceptile, Swellow, Donphan, Corphish, Torkoal, Sableye, Infernape, Torterra, Starapter, Gliscor, Buizel, Aipom, Gabite, Pignite, Krokorok, Boldore, Leavanny, Braviary, Oahawatt, Scraggy,
In addition, I would have had Team Rocket keep their pokemon rather than releasing them or leaving them at James' houses (basically scattering them everywhere. If they wanted to store them, store them all in the same place as they seem to be doing now).
Going into 6th gen team Rocket would have in storage at RT headquarters....
Jessie: Wobbufet (caught not traded), Lickitung (She kept it), Serviper, Yanmega, Frillish, Woobat
James: Cacnea (He kept it), Chimecho, Yamask, Carnivine, Mime Jr, (Never would have given him Amoongus).
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As for XY....
I would have made it a little more badass, sort of like the Black and White game trailer.
Ash would have received an egg from the dragon village at the very end of B&W which hatched into Goomy in XY.
I would not have given Clemont Bunnelby. Instead his main pokemon would be Heliolisk, with Dedenne and Chespin also on hand.
Clemont would drop the whole bad experiments going wrong gag. It got old real fast.
I would have made Serena more interesting. Her goal would be to make movies, and so she follows Ash on his journey and documents it with a video camera.
I would have given Serena a Noibat that's cute and shy, and maybe evolves but not for a long time.
I would make Team Rocket appear less often.
I would make Ash have more battles with random people. He only ever battles gyms, main rivals or bad guys.