You do realise this is a game designed for children right? Game Freak are never going to make a Pokemon game where you play as villains. Do you know how grief parents would give them for having a protagonist that promotes crime?
I do like the idea that you can obtain Pokemon without using the regular method. It's already been done in spin-off games so it should be fine and it would be a lot easier to catch Beldum/Metang/Metagross.