Now, I don't believe you can really run a OYW game. But here's my idea: The protagonists are part of a special unit. Each one has an experimental Gundam, which is a testbed for a unique system.
One guy gets the Beam Rifle, another gets the I-Field, another gets the transforming machine and the last dude gets the Beam Sabers. Eventually, the most successful unit will be mass-produced as their faction's grunt. (So basically, the PCs directly affect the course of the war by contributing to the design of the GM.)
Meanwhile, the PCs are deployed as a kind of superweapon counter, to take on experimental units, Mobile Armors, and to wreak as much havoc as possible behind enemy lines. They have a certain amount of discretion, but they need to show that they're doing damage.