From a gameplay perspective, they probably make the protagonist balanced because you gain them first, and often have to work with a limited number of characters in the early portions of the game. They have to be fairly balanced because the game dictates it: you don't want to be rocking the first town with your protagonist being an 'all offence, no defense' type character.

Having said that, I'd love for them to subvert this. FFVI kinda does with Terra, who is far more comfortable using magic than she is physically.