I'd like to see seperate command structures, as follows:
Civilian Government: Admin skills (R&D/Mining/Production), loyalty, team skills (diplomatic/cyber/etc.)
Fleet: Ship Command skills, loyalty, team skills (diplomatic/cyber/etc.)
Ground: Ground Command Skills, loyalty, team skills (diplomatic/cyber/etc.)
Basically, each path or structure would have its speciallized skills, followed by general skills that any officer/leader could have. Only ground officers could command ground units, only fleet officers could command ships or fleets, and only government officers could govern planets or sectors. Any of the three could join teams. Possibly, any retired fleet or army officer could join the government command structure.
This is kind of complex, but it is more realistic. In my fiction, I generally account for officers in "civilian" leadership roles are either advisors to the civil government, or leading the military's contribution to joint civilian/military efforts.
As you say this is complex and the division between command structure would vary with government type. Some governments may not have a civilian arm for example (would Pax Utopia have a military arm?
). You will probably need a lot more military officers than civilians in any event. An easier option may be to have different titles for the three varieties of commander and give each the title that best suits his/her skills but leave them all in one command structure. Its the multiple command structures that would add the most complexity. Perhaps another option is to allow the player to designate a percentage split between the three types of commander and weight the skills as you noted above (but still have one structure).
Steve