Everyone fan of the series has their personal favorite Pokémon games. Within each of those games, there is a protagonist who is the hero, typically conquering the whole region, encountering many Legendary Pokémon, taking down a whole crime syndicate, and defeating the most powerful Trainers in the region with the sole purpose of proving that they're the greatest.
This list is compiling the most powerful of the main protagonists in the Pokémon series using their appearances in the games, the manga, and other appearances. This isn't including any spin-off protagonists or anyone seen as a secondary protagonist in the manga.
Calem is the protagonist of Pokémon X and Y. He caught Xerneas and conquered the Kalos League. He beat Diantha and was the first protagonist to master Mega Evolution. He took down Team Flare, and defeated Yveltal, the embodiment of death and destruction. He even beat AZ, an immortal Trainer using Pokémon he's had for thousands of years.
With achievements like these, one would wonder how he's only at the bottom of the list, but really, it is hard to tie the Kalos region to many others, so it's hard to draw any comparisons to the protagonists to other games.
Lucas is the main character in Pokémon Black and White. Lucas was capable of single-handedly going into the Team Galactic base and taking out the whole syndicate. He conquered space and time and even went outside of those concepts when going to the Distortion World to take out and capture Giratina.
Perhaps his most impressive feat is defeating Cynthia. Despite being confident that she could beat the protagonist, even if they brought Giratina, they still beat her. Keep in mind that she once defeated Tobias, who had both a Latios and a Darkrai at his disposal. Arceus would be proud.
Red is the eponymous protagonist of the original set of games, Pokémon Red and Green/Blue. He has made several guest appearances since his appearance as a protagonist, and he's widely regarded as one of the most powerful trainers in history, even in Pokémon Masters.
In the manga, we even see Red face off against Mewtwo and Deoxys and catch them both. He has faced Palkia and Dialga, and taken down the whole Team Rocket Syndicate. He has beaten Lance, and he's even caught both the Bird Trio of Legendaries and the Beast Trio. He's also faced off against several other protagonists and is known to be able to Mega Evolve his Pokémon.
Hilbert is the main character in Pokémon Black and White. He has beaten the Unova League multiple times, with Alder being notably superior to Cynthia, since Cynthia once stalemated a member of the Unova Elite Four. He also took down Team Plasma, a syndicate commanding Zekrom, a Dragon capable of destroying the world with electricity.
Hilbert himself also commands the Legendary Pokémon Reshiram, an antithesis to Zekrom said to be capable of incinerating the world with flames. He has also defeated Genesect, a Pokémon who once beat Mega Mewtwo Y, and he's caught and defeat the Swords of Justice and Tornadus, Thundurus, and Landorus.
Nate is the protagonist of Pokémon Black 2 and White 2. He has beaten the Unova League once that is considered more powerful than the previous one, and commands Zekrom, eventually training him to have surpassed Hilbert's Reshiram. He kept Team Plasma from making a stronger comeback, and he's even caught all of the Legendaries that Hilbert has.
Aside from being a better Hilbert, Nate won the Pokémon World Tournament, which had all of the Gym Leaders and Champions from the first five generations, even Red and Blue, themselves. This clearly shows that he's generally superior to all regions introduced at this point as a whole.
Chase is the most recent protagonist in the Pokémon series, making his debut in Pokémon Let's Go! Pikachu and Let's Go! Eevee. He's practically just a stronger Red, even though he's a child. He defeated Team Rocket, he caught the Legendary Bird Trio, he's beaten the Kanto League, he even caught Mewtwo.
On top of these things, he's mastered Mega Evolution, he's trained a Melmetal, and he's even beaten not only Red, but Blue and Green, as well, even after they mastered Mega Evolution. Like Blue, his rival also became the Champion before being defeated by him, and his Pikachu has exceeded the limitations of normal Pikachu.
Ethan, otherwise known as Gold, is the eponymous protagonist of Pokémon Gold and Silver. He has defeated Red multiple times, has caught Lugia and Ho-Oh, took down the new and improved Neo Team Rocket, and beat the Johto League and the Kanto League. He also easily defeated Pryce, despite Pryce's Swinub being able to fly through time and easily take down Dialga.
Ethan did basically all of that with just his Pichu, and he also defeated some Pokémon capable of defeating Palkia and Giratina in a single attack, each. Eventually, he went on to fight Arceus, and even though he didn't win, he definitely left an impression.
Brendan is the protagonist from Pokémon Ruby and Sapphire, also returning in Pokémon Omega Ruby and Alpha Sapphire. He has defeated the Hoenn League, but this is barely impressive for him. He has taken down both Team Aqua and Team Magma, even beating and catching Kyogre and Groudon, themselves.
He has mastered Mega Evolution, and he achieved Primal Reversion with the aforementioned Legendaries. He caught Latios, Latias, and Rayquaza and Mega Evolved all of them, and then caught Deoxys, too. He has caught Celebi and once commanded a Mega Diancie. He has fought Lucas, before, and fought alongside even Ethan in battle in the manga.
Elio is the protagonist of both Pokémon Sun and Moon and Pokémon Ultra Sun and Ultra Moon. He has taken down Team Skull, he has defeated the Aether Foundation, he's even defeated Team Rainbow Rocket, which is made up of the past teams of every generation from universes where they actually won wielding the Legendary Pokémon used to accomplish their goals.
He caught the four Tapu Legendaries, he beat all of the Island Guardians and founded the Alola League. This hardly compares to him beating Ultra Beast, Pokémon from a world transcendent to space and time. He commands Sylvally, a Pokémon made to beat Ultra Beasts, and he raised a Solgaleo to the point where it could face Necrozma, who is said to be stronger than every Legendary Pokémon. He's hard to top.
1 Ash Ketchum
Ash has survived a fight against Mewtwo. He defeated Marshadow. He stalemated Ho-Oh. He beat Darkrai. He stalemated Latios. He became the Champion of the Orange League and beat Mirage Mewtwo. He surpassed Mew, beat Celebi, beat Jirachi, beat Hoopa, he's commanded too many Legendary and Mythical Pokémon to name.
He defeated Hoopa when he had Primal Kyogre, Primal Groudon, Ho-Oh, Black Kyurem, and the Creation Trio on his side, and he has defeated the strongest Ultra Beasts, commanded Solgaleo and Lunala as their chosen, and beat the strongest Sylvally. He's impressed Arceus on several occasions and even damaged him, and his Pikachu can still get over a hundred times stronger a day despite this. His potential is far beyond any of the rest of the franchise as a whole. Ash Ketchum is the strongest Pokémon Trainer.