[@Regitnui]I know I wasn't clear about it before, but I would consider player owned pokemon to be a form of player character.  Because of that, you technically godmodded mine and [@Harmony3812] 's characters, with her Skarmory and my Umbreon (at least I think Fuji was the one that said "Prince.")

As for my pokemon, I don't mind if people generally treat Barley and Fuji them as NPCs as long as they get their personalities right, and only really care about Peach, as she's basically treated as a human.  Barley is Proud to a fault, as his family have served the royal family of Kanto for 200 years, and would act as if you were beneath him if you tried to one up him.  If you persisted, he would take you out quickly just to prove he was superior, trying to break you mentally if possible.  Fuji is playful.  But all three of them are loyal and understand that they need to keep his identity a secret, so they would call him "Master".  Fuji might call him "friend" depending on the situation, but wouldn't reveal his identity to a stranger.