Just FYI, but here's how I currently play the game.
My fleet uses what we call a "Merit Based Command" system.
What this means is that:
--- I set the minimum rank for all of my ship classes to be the lowest (Lt Commander)
--- I put the officers on auto-assign
--- in my current game, I set the tour length to 6 months.
What I'm hoping this does is put the officers with the best skills into the commands. What I want for instance is for my best Survey commanders to automatically be assigned to the survey ships. I don't really care what their 'rank' is. I just want the best survey officers in command of the survey ships. The only time I try to assign officers to a specific job is when a Construction Batt is being sent to alien ruins, I will find an officer with good Xeno skills to command it.
For me, as Admiral of the Fleet and Grand Pooh-Bah of all Colonial and Space Operations, I've got other things to worry about than micromanaging where Lt Commanders are assigned. So, what I want is a simple, no-hands system that puts the right skills into the right places. Or, in game terms, I want my staff and subordinate officers to handle this and not to bother me with it.
I'm sure there are others who get more into this, and I can see where this adds flavor to the game. But I just want a simple, automated system that is flexible in putting the right skills into the right jobs. In my fleet, if the best engineering officer is a Lt Cmdr, then I still want him handling engineering on the fleet's most important ship. I assume there's some way to give him/her/it a temporary rank, or that in general that any complaints about his/her/it being of 'too low' a rank for the job are met with a direct command from the Grand Pooh-Bah of the fleet to shut up and deal with it and that any who complain or bug me about it are just telling me that they aren't really the officers I want in my fleet.