I always feel like these "ideas" get sucked into a vortex and never get read. That being said, I'd love to see missions (both PvP and PvE) in which we can board enemy vessels and fight our way to the bridge. Captain dies, game over for his side. Maybe ship loot could be available to the victor as well.
I sort of thought this is what "boarding" would entail when I read about the game including the ability. The interior of each ship class could easily be "mapped" and it would satisfy the raid desires of many PvP'ers. The interior could be an instance to enter, so I'm not sure it would be difficult to do. Would also allow us to integrate ground combat skills into ship combat in a more dynamic way. Just food for thought tossed into the abyss.