A solution I have to some of these issues is to create a large collection of fighters and PDCs that Lt-Cdrs take control of. This way, all of my junior staff have something to do. I also don't suffer from the clearing house every 6 years.
An additional plus of this is that these junior staffers gain skill constantly. Many of them end up being fighter aces (though this was especially true in 6.2 with the glitch, it is still true in 6.42... just within reason), even if the fighters in question do not have guns.
This is one of my game start "fighters". I don't even have weapons on it, and they're dirt cheap to build. Run off 200 of these, and you'll never have an officer sitting idle.
F-0a Trainer class Fighter 130 tons 1 Crew 22.9 BP TCS 2.6 TH 15 EM 0
5769 km/s Armour 1-2 Shields 0-0 Sensors 1/1/0/0 Damage Control Rating 1 PPV 0
Maint Life 0 Years MSP 110 AFR 0% IFR 0% 1YR 0 5YR 0 Max Repair 7.5 MSP
Intended Deployment Time: 0.1 months Spare Berths 9
Jones Aerospace 15 EP Ion Drive (1) Power 15 Fuel Use 155.65% Signature 15 Exp 12%
Fuel Capacity 5,000 Litres Range 4.4 billion km (8 days at full power)
This design is classed as a Fighter for production, combat and maintenance purposes
You will also want these:
Fort Hampshire class Planetary Fighter Base 3,850 tons 57 Crew 393.6 BP TCS 77 TH 0 EM 0
Armour 5-21 Sensors 1/0 Damage Control Rating 0 PPV 0
Intended Deployment Time: 3 months Flight Crew Berths 1
Hangar Deck Capacity 2500 tons
Fuel Capacity 250,000 Litres Range N/A
Strike Group
7x A-2 Tigershark Interceptor Speed: 6250 km/s Size: 6.4
This design is classed as a Planetary Defence Centre and can be pre-fabricated in 2 sections
This PDC can hold 19 of the trainer fighters, so you don't need more than 11 to hold your 200 trainers. It is also useful for later when you have real fighter craft, as you can see above.
Simple solution to the idle officers issue.
That being said, I also support the idea of having bridge crew. I want a Sulu and Chekov, not just a Kirk.