I think the reason is quite simple really. The Pokemon world is intended to visualize what life would be like if more living beings strived for peace and good morality. Its a world where life, though certainly not perfect, is in many ways better than our own. Its part of the very engine of their society to form natural and pure bonds with Pokemon, and to do that it makes sense for Pokemon to start off naturally "good". From that perspective, its got nothing to do with just kid-friendliness. I don't have any problem with Pokemon being initially good, and its kind of concerning that the boundaries are stretched occasionally, or when they fail to show the reasoning when a Pokemon does bad against their nature. (Litwick, Scrafty, etc).
I am the current leader of Save Our Voice Actors, a Pokemon fan group supporting the voice actors in the anime dubbed by 4Kids (seasons 1-8). Our goal is to provide The Pokemon Company international with encouraging feedback in support of returning the main cast members. If you're interested, please visit us at facebook.com/saveourvoiceactors