Ok, its not which army is going to win, its which army the Sith WANTS to be the winner.
Palpy is a pro-human person, and CIS is non-human oriented in terms of ownership and major sponsors. Obviously palpy will want the clones to win instead.
Also defeating the CIS would make great media work concerning non-human aliens are evil, rallying more "good human" to palpy's side.
It really is that simple. Though I think Doku may actually WANT to win the war and take the Throne by himself.