well, ships could be like, pilots can only use fighters / bombers, and only Freders can use capital ships.
other then that, you could have cards like "surface bombardment: Lucifer" 'effect, target member of 8 points or lower is send to the ban pile" and such be usable by everyone
fighter/bomber cards would give pilots eather more attack/defense, a special ability like "Ship card: GTF Perseus" "effect, target pilot can negate one attack due to his ships Uber speed"
capital ship cards would help freders make better "campaigns" which would be stacks of "freder cards" that do the effect of all those cards at once but it takes time to fred a mission or campaign that makes it posable to destroy it with a card like server crash. The freder or campaign cards, would also have super ablitys that work only if you have say 2 cards with this efect on it in the campaign such as the Iceni and a knossos portal, would unleash a ability called "Shivan Super Fleet" or something like that that would force all members be sent back into players hands or force them all to the top of the players decks.
oh and the "ban pile" was my idea