Falkner was just to early in the game to let him have lv 15 pokémon like Brock's onyx. =/ In RBY, LGFR, you had the Viridian forest to train, and the battle with Gary, who's pokemon were already trained. The ??? trainer in GSC's pokemon was not trained yet. And unless you fought billions of Sentret or Hoothoot, your pokemon would have about lvl 10 (for the starter) and 8 for a caught pokemon when you reached Violet City.
The gymleaders in Jotho had lower lvl's, but their pokemon were quite annoying. Pidgeotto, Scyther, Miltank, Gengar, Steelix, Polywrath, Dewgong, Dragonair. The gyms in Jotho were usually double-typed, like Dewgong is an ice and water pokemon. Their weakness and resistance isn't always like the 'pure type' the gym is based on. That's why their lvls are lower, I think.
Also, the road between Violet City, Azalea and Goldenrod town, is not that filled with challenges such as Mount Moon was between Pewter and Cerulean. The number of rocket grunts in Slowpoke Well is lower than in Mt. Moon, There are no trainers in Ilex forest.... Unlike the road to Cerulean City.
That's why Misty's pokemon (who's second gym) are like than Whitney's (who's third gym).
At least, that's what I make from it. could be wrong, could be right, it's just a thought.