Hmmm... true, the "look-wise" is awkward and pointless... *goes to remove it*
However, while you do have a point about the other one, I don't fully agree. Charmander is very young and hatched in captivity (although that hasn't been mentioned in the fic yet). He knows what Pokémon training is, and he knows the Agreement, but he's never gotten to know what an abusive trainer really is. His mental idea of a bad trainer is more like his previous trainer, who just keeps him in a Pokéball and then uses him to trick somebody else. He's never known abuse, nor heard stories about it, and doesn't exactly picture a human kid, much less one who saved him out of the rain, as somebody he should be wary of.
Still, it's true that he'd probably take more time into the decision, since he does know what he is agreeing to. I'll probably change that in the next revision (if I know myself correctly, there will be one, but otherwise I'll just change it sometime later when I'm doing minor rewordings and fixes).
The Gym of Legendaries doesn't have to do with the prologue directly, but it does have to do with a side plot, since the Cleanwater Gym's purpose is not only being a random Gym.