I was thinking about the idea of spaceships as mobile home bases when I came across another post talking about the emptiness of space fights at the moment. That got me thinking about how they handle space fights in most movies and anime -- often, fights happen around giant capital ships, which serve as the 'battlefield'.
So, I wonder if that could be done in GH2? Conceptually, flatten the ship to two dimensions. Attacking mechas land on it and fight on it; they can also step off the sides and fight 'around it' there, since it would sort of be like an island floating in space. It might also have some turrets on it that would fight for the defending side (which could be targeted and blown up individually.) Maybe an airlock or two from which new mecha emerge under the right circumstances, or into which mecha can retreat.
In multi-part missions, you could even fight your way up to the airlock and use it to enter the enemy ship directly.
You wouldn't "attack" the larger enemy ship, probably, aside from blowing up turrets; once you defeat every enemy mecha standing on the battlefield, you'd be assumed to have 'won', and what happens then would depend on how the fight started (but blowing up or capturing the enemy ship could make sense if the attackers win.)
There could be one battlefield defined for each type of ship; that way, the PC's ship could be "attacked" and play a role in the fight without overshadowing the mechas. If players are able to modify ships, then things like turrets could be added to make them show up on the battlefield.
There would also, most importantly, be things sticking out and such to provide cover. Forests of sensor arrays or whatever.