My Version of the Pokémon Anime

However, you can suggest things in the comments.

Overall

 * Pikachu wouldn't be restarted every region. Instead he just wouldn't be used as much in the beginning of each region while Ash trains his other Pokemon.
 * Also, Pikachu would get a Light Ball during the Johto saga in order for it to suck Pikachu's excess electric power out, otherwise Pikachu would gain too much power and he would explode.
 * I'd reveal Genders for characters' Pokémon.
 * Treat Ash's Grass and Water starters better. Bulbasaur and Rowlet didn't want to evolve, Bayleef was pretty childish, Sceptile had problems battling thanks to being rejected by a Meganium, Torterra always lost after evolving, Snivy struggled in a couple of battles, and almost every one of Ash's Water starters never evolved.
 * Time would pass, and the characters would age slowly. For example, Ash would be 10 by the start of the series, but by the time they get to Johto, Ash would be 11.
 * Make it less childish.
 * Better character development.

Original Series

 * All of the badges would be won fair and square.
 * In the Pokemon Tower, a Cubone mourning over its dead mother (like in the games) joins Ash's team. It starts out like Ash's Larvitar, not trusting Ash or anyone, but eventually grows to love the gang. It later evolves while protecting multiple young Cubone.
 * The guns are edited out of "The Legend of Dratini," so that the episode isn't banned, thus removing the plot hole involving the capture of Ash's Tauros.
 * The seizure-causing strobe lights in Computer Solider Porygon are removed altogether, thus adding Porygon and its evolutionary family to the series (Porygon was wrongfully blamed.)
 * Bulbasaur should have evolved into Ivysaur and learned to like its new form, giving Ash the Pokémon Trainer's team in the Super Smash Bros. series. It would evolve again sometime during the Orange Islands.
 * Gary, A.J, and Ritchie would all be Ash's main rivals, and appear as much as Paul and Barry do, so that they're developed on much more.
 * Ash's Primeape appears more often and stays on his team instead of being given away after four episodes.
 * Brock would get Togepi instead of Misty thanks to him wanting to be a Pokémon breeder. In addition, Togepi is much more useful, evolves earlier, and isn't released.
 * After protecting the Pidgey from the Spearow, Pidgeot should have still been on Ash's team.
 * The Orange Islands is changed to the Sevii Islands.
 * Ash would one catch one Tauros in the Safari Zone instead of 30. He would also catch a Rhyhorn, an Exeggcutor, and a Dratini during this time.
 * Ash would catch an Eevee with a personality similar to Red's Eevee from the Pokémon Adventures manga.
 * Eevee later evolves into an Espeon to contrast Gary's Umbreon.
 * Instead of Gary having both Nidoking and Nidoqueen, Ash has a Nidoqueen, while Gary has a Nidoking.
 * An actual Team Rocket arc with the admins and Giovanni. The TRio would remain, however.
 * Tracey should have come along to Johto with the group. In addition, Tracey's Scyther and Venonat should have evolved.
 * Ash would have transferred his Kanto team (except Eevee) to Oak right before he left for Johto, so that they don't steal the limelight.
 * The Johto arc is redone so that there's no filler.
 * The GS Ball is saved for the fourth movie.
 * Misty captures Totodile instead of Ash, and Ash gets a Wooper, which later evolves into Quagsire. Totodile also evolves.
 * Misty's Horsea should have evolved.
 * Instead of Misty having both Staryu and Starmie, Misty would only obtain Staryu and later evolve it to Starmie.
 * Brock's Geodude should have evolved.
 * Ash's Phanpy and Cyndaquil should have evolved instead of waiting until Battle Frontier and Diamond and Pearl.
 * Brock would leave after the original series.
 * The Silver Conference is changed to a second Indigo Conference.
 * Ash should have won the second Indigo Conference and left the show to protect his title.
 * A female character named Jodi (think of her as the early version of Leaf from FireRed and LeafGreen) should have been added to the team.

Advanced

 * The series starts to become more like the games and the manga, with levels, natures, characteristics, and all teams with fully evolved Pokemon.
 * They would have followed the Emerald plot with Aqua/Magma, and have Rayquaza come in and stop it all. No Pikachu getting possessed, Maxie would NOT be that polite, Steven would replace Lance, and so on.
 * May should have caught a Swablu.
 * Max's character isn't so boring, because why add him to the team if he can't do anything? Also, he is given some Pokémon. (I mean we see young kids in the games having Pokémon for Pete's sake!)

Thoughts

 * Dawn's Piplup and Buneray should have fully evolved.
 * Dawn's Piplup is made to be less of an Ash's Pikachu clone, by staying in his Poke Ball and evolving.
 * Dawn catches a Budew, which evolves into Roselia, then into Roserade.
 * Shorten the one year gap between Snowpoint and Sunyshore.
 * Ash/Lucas's Gible shows up in the middle of the anime, instead of not showing up until near the end. Gible also should have fully evolved.
 * Gible would have the same Draco Meteor story, but the imperfect Draco Meteor would hit Lucas, Barry, or the COTD instead of Piplup. Gible would evolve when it finally mastered Draco Meteor.
 * Dawn catches an Aipom on her own. In addition, Ambipom would stay on the team.
 * Dawn's Togekiss would be recieved as a Togepi egg so that she doesn't feel like a last minute eddition. Togepi would evolve both times during the HeartGold and SoulSilver season.
 * A HeartGold and SoulSilver season, where Team Rocket teams up with Team Galactic to destroy both Johto and Sinnoh with the power of Arceus, and Lucas and Dawn have to stop them. This is Team Rocket's final arc, where after this they eventually disband for good (The TRio would also make a cameo). At the end of the season, it is also revealed that Ash went through a Heroic BSOD when he got defeated as a champion sometime after the original series, secluding himself on Mt. Silver, and becomes like Red as depicted in various fanarts when he comes back to his senses. His team would be similar to Red's team, but Espeon replaces Lapras.

Thoughts

 * Ash/Cheren's Scraggy would be caught normally.

Thoughts

 * Loosen up the filler between the second and third gyms.
 * An Omega Ruby and Alpha Sapphire season, where the gang travels to Hoenn and has to help Brendan, May, Wally, and Max prevent their planet from being destroyed by an incoming meteoroid.

Thoughts

 * It isn't so confusing.