What I see, in terms of officers and their ranks - the player can alter their playstyle after, say, a decade - if previously fighters were not used, and the focus was on large ships, complete with bridge and all the auxiliaries, you need 1 higher ranking officer and several Rank 1 officers.
But, say, suddenly, player changed the strategy, now fighters are making up the majority of the military shipping. Such as 1 Large ship and 100 fighters. So, the ratio at this point becomes 1:100...
Do correct me, if officers provide bonuses when bridge is not present...
Either way, the 1:3 rule is... lacking.
The biggest gripe for me, is that only lowest rank officers can take auxiliary positions. If we had more liberty in assigning specific officers...
Or say, how about allowing scientists take the command of the science module on a ship? Though, I suppose that may have been relevant back in VB6, when we still had geological and other teams, with various officers...
I am not sure if ratio controls for player would... solve much. It kind of limits them, as in, makes them stick to an old doctrine... Although, if early game you made a ratio like 1:2, akin to low amount of auxiliary modules researched, then you change it to 1:10 after a decade, when the research of auxiliary modules and proper fighter modules are completed. I suppose this may be an option.
Or, how about setting the desired number of certain ranking officers manually, making the autopromote/demote try to fit the needs you set? I personally never made it to +1000 officers scattered across multiple systems, so I assign officers manually, but, if someone has a need...
Either way, commanders would be less of a problem, if I could assign higher ranking officers to auxiliary station positions (Engineering, CIC, etc.). Right now (V1.13) you can assign higher ranking officer to a ship itself, but not to the ship's auxiliary system.