How about a captain MP mode, similar to commander battles in mount and blade Warband.
Each player chooses one ship, perhaps all limited to the cruiser level. And you have like, 8 (or more or less) players on each side, so 16 players with one ship.
And either allow them to choose from any faction, or the faction is randomly chosen for both sides beforehand and then the player chooses a ship from that specific faction.
Just something i think would be quite fun.