I believe that Natalya will win. She has that Longivus corvette thing and the Armoured Core. She wins.
Ideas on battles: A rescue mission is always fun, as the captive is often slaughtered hilariously. In massive battles like these, kill all gets boring at the end with one little space ninja hiding across the field from everyone and then you have to go get him. So an objective is best.
Or to assassinate the enemies leader.
I love those games.