You know there is a concept called balancing . The game would have to be less about grinding (fighting wild pokemon for experience) and more about linear progression, sure. One thing you could do, for instance, is the gym battles or elite four could have pokemon 2-5 levels higher than your highest leveled pokemon in your party no matter what level your pokemon are (just as an example).
Also, on my HG game at the moment, my pokemon are all level 58 (only the 4 that I battle with, and the other 2 are for HMs). This is right after battling Blue/Green for the earth badge, and I very rarely ever battle wild pokemon.
So, in conclusion, having pokemon being level 100 by the time the 3rd or even 4th region comes around is simply not true. . Leveling just gets harder and harder! (depending on the pokemon's experience type) Have you played any of the pokemon games??