I think the capships need some sort of point defense weapon to defend against single and double missles, but wouldn't be as effective against swarms. Maybe a battery of flechettes in pods that would fire against incoming hostile missiles or targets if they got too close?

I think that the key to the whole anti-missle thing would be to make missles/rockets destroyable first. :P

I would like to see Guild Wars.Like the pirate guild and the viper guild fighting. I would LOVE to be a tactician on a battle ship. Also A command ship could have a speacial in-sector map. So you can see all enemy units that are visible on radar.