Personally I think a hybrid of the two would be a better use of time, with all of us chipping in on the running and management of the "background" items such as economy, with a ship allocation for example to allow for "fleets" lead by individuals, or groups of individuals, to be formed. Of course deployment would be a group thing but fleet composition can be as the admiral wishes it to be.
Saying that though, if there is a lot of people the number of fleets would be limited. Performance and activity bonuses?
The advantage with this is that there's no danger of things tripping up to too great a degree should someone go missing for a while, though its added beaurocracy in essence.