I don't know if someone's already mentioned this idea, but here goes.
Instead of the typical damage model of each ship doing x damage to a target and the target blows up after taking y points of damage, how about the target being destroyed after being hit z times?
Here's what I mean: Let's say you have your 2,500 ship blob fire upon a base using the new damage model. The base can take 25,000 hits before going down. It doesn't matter how much damage each of your ships do (or is it does?), what damages the base is how many hits it takes. So with the example case, your blob will have to hit the base with 10 volleys to destroy it.