While you’ve been traveling all around the Kanto region, the various Gym Leaders that you’ve defeated have been secretly training to keep up with you. Once you’re the Champion, you can rematch the Gym Leaders at their original locations. You can also battle each of them again when a new day starts.
It’s not just the Gym Leaders that have been getting stronger. If you return to Indigo Plateau, you can re-enter the Pokémon League and challenge the Kanto region’s elite trainers, at their full and unbridled strength.