C&C had a sole survivor game, where you literally controlled one unit on a map and had to hunt down other units. For Homeworld this might be a little limited/one sided, so how about mixing it up with the popular gun game from FPS’s?
Each player starts off with a single lowly Scout. Each kill gives you the next ship up (so Interceptor etc) until you end up with whatever is deemed to be the most sensible end-game ship (Battlecruisers etc). Self repairing by the larger ships would probably have to be disabled, but it could be an entertaining mode.