I guess it doesn't matter all that much what method you use to determine the winner. Whatever you choose, the better players will just adapt their strategy to suit the situation.
Even by adding the latest restriction to the rules concerning outfitting ships, people are still going to build ships which maximize their score/cost ratio as opposed to ships which would be most useful in battle. I wasn't the one who sent in the score obtained by 2000 empty battle stations, but that's just because I hadn't gotten to turn 150 yet.
Now we have to pretend that what we're building has some use. It seems a bit contrived, but if they say I just have to fill the hull, I'll be creating an empire-wide shortage on organic armor.
(now there's a balance idea - make components more expensive the more you use them, heh)
-Drake