And there are no weapon "slots", you just buy stuff until you run out of Cp for that ship class, but I can see your point.
I believe Halo3000 himself actually came up with the solution last night. Unfortunately, groggy as I was, I can't seem to recall anything more than every ship having a base engine for free, and THEN the player may buy more engines if he/she so wishes.
He did this for his Shortsword Frigates, which he designed to be almost like overly large Fighters; very fast (12" movement), but cost efficient and lightly armed.
It's certainly a cool idea, but I'm not sure how much good it will do him in the end in an actual game.
Oh, and as long as we're on movement, what would you guys think of adding in a rule in which your ship can use half of it's move to turn 180 degrees if it has a move of more than 4" (just because turning at the moment is kind of bleh)?