I think it's because you fight him before the Kanto gym leaders so they made the game more of a challenge to the end. It wouldn't really make sense if the Kanto gyms were really easy to beat because it's not really a part of the Postgame, It's still kind of the main storyline.
I also came up with a different explanation, Maybe he was just training a different team as you fought him for the title of the Johto League Champion? It would make sense for him to train new Dragon types since he is a Dragon trainer; And what kind of Dragon trainer wouldn't switch their team up once in a while? And also in Fire Red / Leaf Green, On the Fame Checker's information of him, It says; "I'm considering going back to my hometown. I want to retrain my Dragon-type Pokémon and strengthen them.I'd like to invite you to my hometown someday." So he does want to Re-Train his Dragon types, Maybe he got new ones along the way when he became the Johto Champion?
I hope this explained it in some way!