im intrigued.
i think that slightly better than just doubling the stats of the enemy ships, doubling the NUMBER of ships might be better. the way the ship damage and health are calibrated for the weapons would be all messed up. if you are sitting there and the ship can just absorb clip after clip of gatling and never having a hull break, the guy on the mortar is sitting there bored. while the engineer has no reasonable chance to keep their armor and parts repaired.
the way forward in my view would be to make more enemy ships spawn. firstly because in all fairness a good pilot can dance around a enemy ship for ever if there only one of them, no matter how powerful. increasing the number fo ships means that the pilot must be aware of more things. the engineer as well has to be on his A-game because more ships are shooting at them, so more dancing from part to part, which is more fun than camping the hull... also i think the feeling of facing a huge armada with just your little ships and kicking their butts would be better than grinding down a couple ships that are the same boring few ships from before but taking twice as long to kill. also i think there the ability to destroy the armada ship by ship will be more interesting and emotionally rewarding ebb and flow to the battle