I know it would be next to impossible to add a whole new dimension to the game this far along, but I've always liked the idea of being able to raid other players ships.
I realize that this would apply primarily to capital ships, but I still think it could add some interesting new strategies to the game. You would have to build special transport crusiers that carriered large boarding partys, but were not very heavily armed. They could have the ability to launch pods, or attatch some sort of raiding tunnel, to enemy ships and then attempt to take them over completely, shut them down for a period of time, or cause some damage via explosives and sabotage. While onboard, the the soliders could cause a small drop in overall efficency of the ship they're raiding.
This would require a hunge amount of other factors in order to function properly (ie. Hiring secruity officers for your ships, adding technologies, tweaking the AI etc.) but I thought I'd post it anyway!
Thanks for a fantastic game Stardock and Ironclad!