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See how much fucking bigger RBY is? It's like comparing an open world game to a rail shooter.
Because of the Gameboy's hardware limitations and the scope of Crystal, the region of Johto is considerabley more compact than the original Kanto region found in Red/Blue. Further, the Kanto region in Crystal is also more compact.
The result was less time spent in between gyms, meaning that your Pokemon were usually lower level. To counter-balance this, gym leaders were lower leveled. Kanto gyms were probably stagnated in order to allow the player to use new Pokemon without having to grind.
