Overall, I really like the new officer system, but I don't think it works as well for things like mining and stabilization as it could. The problem is that while "you've been promoted, now we're kicking you out to wait for a command at your new rank to come open" is great for warship officers, it doesn't work for officers specializing in other things. Unless you build a second design with senior commander selected or something, pretty much all of your civilian ships are going to be at your lowest officer level. So someone who specializes in those things ends up out of a job after they get promoted. Yes, I could give them a command hierarchy position, but there are a limited number of those, and because the game doesn't actually recognize span of command, at some point, it's actually adding micromanagement and reducing the numbers. The same happens, to a lesser extent, to survey officers.
So how to solve this? Add another checkbox to the Ship Design window for flexible command. This would let the maximum rank on a ship go up to one rank over the minimum. There's a lot more reason to insist on a strict hierarchy in combat units than in something like a mining operation.
(And yes, I know about the "do not promote" box. I don't want more micromanagement.)