Like what Hopeless said above, the anime has shown that having a legendary doesn't make a trainer impossible to defeat. Tobias, the trainer who won the Sinnoh League, had two legendaries, one of which (Darkrai) was destroying literally every trainer it was up against and had also wiped most of Ash's team with little effort before eventually being defeated by Sceptile. Pikachu then tied against his Latios, but because Pikachu was Ash's only Pokemon left, the battle ended in a loss for Ash but he still did put up a good fight.