Moving away from the technical side of things and back to gameplay...
One thing that I have decided in my infinite wisdom is that, one: Units should more or less be designable from the ground up, and two: This should have both an effect on gameplay, as well as a visual one, and three: The exact nature of these statistical changes should be kept secret.
For instance, you are designing your uber-awesome airship. You give it flapping wings, thrusters, a large troop quarters, and heavy armor plating, then paint it bright pink. All of these should do exactly what common sense would dictate: the wings would add extra lift and maneuverability, the thrusters would add speed, the troop quarters would increase the number of units you could comfortably fit in it, the heavy armor plating would increase the number of hits it could take, but would slow it down and increase the amount of energy it would require to stay aloft.
None of this, however, should be shown in the form of exact numbers to the player. Certainly, the troop quarters would tell you how many units it was designed for, but it should be possible to overfill it, at the risk of loss of morale.
Too many games with decent customization I've seen fail to live up to what it could have been because either exact numbers were given and thus everyone ended up using the "best" combinations, or the customization had no effect whatsoever on the actual gameplay.
I shouldn't know that giving my recruits steel longswords will add +3 to their attack power, but instead that they're now armed with decent weapons and are thus dealing much more damage.
Players should be expected to play around with the various customization options until they find a combination which fits their playing style.