Now wait a minute here, high level Pokes will only disobey you if you received them in a trade. That was a security measure that GF put into the game to prevent players from starting out with L70 uber Pokes and totally ruining the strategy/playability of the game. I have never had a problem (that I can recall) where a Poke that I raised myself disobeyed me.
As for leveling up your Pokes early on, I think that is a bad strategy. You are much better off bringing along your Pokes normally at first, and then later take advantage of locations where you get battles with lots of Exp points, and helpful items such as Exp Share. Plus it makes the game more of a challenge since the AI is subpar, battling opponents with lower level Pokes helps even out the playing field.
Aragorn gave the best advice, in relation to the second gym. A Taillow with Wing Attack is capable of blowing through every Poke. I suggest using it at Lv17 or 18, just to make it some kind of challenge. Starting with Mudkip, and adding Tailllow, you can get through the first three gyms pretty easily, especially in Ruby/Sapphire. I always do that so I can get to the point of setting up Secret Bases.