Oh god Big Boss would be a terrifying to Pokemon battle battle with. He'd be spouting off all this gar stuff and by the end of the fight you'd say fuck it and join his team.
You know, of course, that those aren't Pokeballs BB has there. Those are obviously Fulton Grenades, since BB does ~90% of his recruiting by attatching balloons to people, so the same would probably go for Pokemon too.