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I know the games, manga and the anime all follow different plot lines. Has it ever been stated in the show as to who the strongest Pokemon Master is? Is it Tobias since he had already captured 2 legendary pokemon and it is implied that he probably has more and legendary pokemon are the strongest.

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Unlike the Pokemon League concept in the games where you battle the elite four after collecting 8 badges, in the anime, the trainers after collecting 8 badges, first compete in a Tournament called the Pokemon League and the winner then gets to take part in the Champion League, where they compete against the Elite four and then challenge the current Pokemon Champion for the title.

The reason for mentioning the same is because, it has to be emphasized that challenging the Elite four and even the Champion, is a lot more complicated in the anime. Hence, making them highly skilled and a lot more overpowered than any other trainer.

Tobias is not the strongest trainer in the Anime. This can be easily disproved with three reasons

  1. Cynthia "The Sinnoh Champion", makes in appearence in the Unova Series after Tobias won the Sinnoh Pokemon League. It was stated that Cynthia was still the champion of Sinnoh. I think that would imply, Tobias didn't defeat her in battle.
  2. Tobias's strongest pokemon was most likely Darkrai considering he used it the most. This was defeated by Ash's Sceptile which is no doubt a high leveled pokemon but it is no where close to the strength of an Elite Fours/ Champions Pokemon. In the same series, we watch Cynthia fight Paul( A trainer with the same level of experience of Ash). His " Torterra ", the starter pokemon that he used and his strongest(Considering he took part in 3 Pokemon Leagues with it). was knocked out with a single blow by Cynthia's Garchomp. The same Garchomp, also defeated Flint's Infernape, which effortlessly pummeled Ash's Infernape and Pikachu. I think it's fair to say Sceptile is certaintly not as experienced as Flint's Infernape and even Paul's Torterra, yet was able to take out Tobias's Darkrai. This sort of indicates that Tobias's Darkrai is no where close to Elite Four tier
  3. During the course of battle, Tobias stated that the Draco Meteor from Ash's Gible would've taken out any of his pokemon except Darkrai. Ash's Gible is no where close to an Elite Four tier pokemon. This again proves Tobias is definitely not the strongest trainer.

If one were to take certain Evil Teams in the Anime, gaining control of a Legendary Pokemon into consideration, it would end up complicating the answer for the same. So disregarding them (Considering the fact that the Pokemon aren't technically owned by them & they eventually lose the pokemon cause of plot), that would leave the Elite Four and the Champions.

  • Although, the Champions can be considered to be stronger than the Elite four Members, it is certainly possible for a few elite four members to be stronger than the Champions of another Region.
  • However, ultimately, the strongest train would be one among the list of champions, so the next task would be to determine which out of all the Pokemon Champions across all the regions, is the strongest.

The answer for the same would Primarily be opinion based as we haven't really seen Pokemon Champions of Different Regions Battling it out. At the same time, Type advantages aren't as significant in the anime, hence eliminating that factor from a comparison.

Hence, the answer to your question would be a No. Since we do know that the strongest trainer is one among the Champions, in the anime, the strongest trainer would be one among the following list:

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