The Pokémon anime has always been about how true strength comes from bonds of friendship, and that a Pokémon has more value than just its raw power level. Or at least, that's usually the case, but Ash's loss against Tobias flipped the script, ruining one of the show's defining lessons for kids.
Even more so than the games, the anime has always emphasized the importance of befriending one's Pokémon. It's part of why Ash never catches that many Pokémon; he can only have a real relationship with so many at a time, so he often ends up with a fairly small pool of very loyal Pokémon in each region. Ash and Pikachu's bond of friendship has allowed them to overcome some truly incredible circumstances, while Ash's bond with his Greninja was so strong that the two were actually able to link minds using the anime-exclusive "Bond Phenomenon." The t desire of Ash and his Pokémon to win is a powerful force that not every trainer has.
Ash's Loss To Tobias's Legendary Team Destroyed Pokémon's Greatest Lesson
In the Lily of the Valley Conference, the grand tournament of the Sinnoh region in the anime, Ash found himself against his rival in the region, Paul. Paul did not treat his Pokémon well, and routinely discarded Pokémon that didn't live up to his bar--that's even how Ash got his Chimchar. With this as their final battle, Ash eventually came out on top with his Infernape's help, proving his method of raising Pokémon to be superior, and that bonds of friendship really are important. Then, Ash progresses to the next round, where he faces the mysterious Tobias. Tobias' first Pokémon is Darkrai, and his second is Latios. While he presumably had six Pokémon, the other four are never seen, because he wiped the floor with Ash in the semifinals using only those two Legendary and Mythical Pokémon, then winning the finals and the tournament.
Tobias isn't given much characterization, so it's hard to say if he treats his Pokémon well or not. Either way, he certainly didn't have as close of a relationship as Ash did with his Pokémon in Sinnoh. Having Ash beat Paul using friendship, only to immediately lose to someone using what any casual fan of the series would see as "Strong Pokémon", undermines the message. It leaves viewers with the feeling that a trainer's bond with their Pokémon will ultimately never be enough to bridge the gap between certain Pokémon's strengths. While that's good for keeping the aura of rarity and strength around Legendary Pokémon, it really just comes across as proving that Paul, not Ash, was right. For the record, when Ash finally won the Alola league, it was when he was using the Mythical Melmetal--which only seems to further prove the power of Legendaries.
Ash's Loss to Tobias Undermined His Victory Against Paul
Fans of Pokémon at the time, and even now, can be quite bitter about Ash's loss to Tobias, given how incredibly unfair it was. Ash was in a good spot to win it all, and his victory against Paul was an incredibly satisfying payoff to a long storyline. However, having Ash lose to a never-seen-again character who essentially "cheesed" him using a fully Legendary team went against everything that Pokémon has been trying to teach to its viewers.
