Yamato (Megaton) is an agent of sorts so it makes sense that he would be taking on Agent 47. This will be a fairly easy battle for him to win though as his mech suit makes him considerably more powerful than 47 any day of the week. I would go as far as to say Yamato could win without the suit but of course the fight would be a lot more interesting. Yamato just has better feats like taking out some mechs on his own. Yamato (Megaton) wins.