I think the best idea, though not the easiest, for that would be like you'd build muscle.  You work the muscle and work and you gradually get stronger (though it would be gradually more efficient in this case).  I agree with Lamma that there would also have to be a scalar value, so that bigger ships are slower until you upgrade their engines and whatev.  Heh, or you could add an "engines" component that would affect the time needed to travel, do missions, etc.  Either for each ship or for your mothership, and the bigger it gets, the more engine power you need.

I still like the stand ground idea, hit and run is pretty much what happens now (minus the overpower), but what about a "grapple" strategy.  Kinda like a cross between SG and Board, they close to transport range, and battle it out with big guns shooting each other, and marines fighting it out inside, but the trick is that the person you're attacking can have more marines and take some of your ships if you're not careful.