Could you please provide an example of how you would set an admin command structure for the OOB that was listed at the beginning of the thread?
I agree that the current system is not very flexible and sometimes will create odd situation as you might not find the leaders you need at different ranks... however you can most often deal with the system most of the times if you have enough officers.
I usually start at Lieutenant, Lieutenant Commander, Commander, Captain, Commodore, Rear Admiral, Vice Admiral, Admiral, Grand Admiral and finally the Void Marshal.
So... small commercial utility vessels get Lieutenants in command, regular commercial vessels a Lieutenant Commander and proper commercial military support ship can even get a Commander in charge depending on their importance and function. So I already have a good use of these commanders here.
Military ships and small structures are...
Fighters and FAC 50-1000t usually are Lieutenants, squadron leaders usually are Lieutenant Commanders (scout and/or sensor variants)
Corvettes and small utility crafts are Lieutenants Commanders
Small capital ships from frigates to destroyers/cruisers are Commanders with Captains as Squadron leaders (flag officer)
Large capital ships like Battleships, Fleet Carriers and Battle Carriers are commanded by Captains and larger task-groups (flag officer) are commanded by a Commodore
For Admin Commands
Commercial Admin Commands usually start at Captain and go up to Rear Admiral in rank sometimes higher.
For military Admin Commands the usually start at Rear Admiral as leaders of Task-forces and then up that chain of command.
I think that you do want some vacancies in jobs at most level as so some "unemployed" are OK... I generally assume they are staffed at HQ and other institutions.
The key is to give different levels of work for officers to both ships and admin commands so you can have the officers work in many levels and spread them out, this works relatively well but you always want some "unemployment" at every level for the system to work. I also don't assume they are unemployed as much as in re-training programs, teachers or administrators in higher commands. Sure it would be nice with work for them to do to say staff admin commands but then you would end up in the same situation or people complaining they can't fill the staff of their admin commands or they have still have too much officers as not everyone will meet the criteria to fill certain slots.
People in your hierarchy are never really unemployed but part of the the bureaucracy and administration machine feeding the more vital and sought after positions. When a ship commander is promoted and put at HQ he or she is likely given some important bureaucracy job or think tank that is as important as the job they had before. Just because there is not game mechanic does not demean the character in the game in my opinion, that is just the position of you as a player when you are "robbed" of someone with a good skill and you feel that you are left out on some potential gain. Personally I'm fine with this from a RP perspective especially if they are promoted for political reasons... they get more pay and don't need to risk their life on a ship any more... win win for them but not you as a player...