I think that it would help the pilot if the airships had a few gauges to measure altitude, speed and vertical movement. Also if all the maps had the same orientation, with the top being towards the north, it would make the compass direction HUD easier to use.
Perhaps the captain could choose to add additional armor (limited by vessel type of course) going for a heavier, more protected vessel but with a speed and maneuverability penalty. Or even remove some to increase those attributes.
Instead of the vessel numbers being equal perhaps you could spread the teams over different numbers of airships. For an extreme example you could have four Squids with three crew each versus one Galleon with twelve crew. Obviously the match balancing would be 'interesting'!