The default TMO crew management eliminates that little RPG element the game had. That is how I look at it, cause I don't know much about real life US Navy ranks - how it worked during ww2. So, I changed the same settings as you - max officers and petty officers for each sub (did that before starting new campaign), and its more interesting now - I have some say when it comes to qualifications. A sailor reloading (and maintaining) torpedoes for 4 years, in war conditions, surely can be named a specialist in that task.
We only need to look at the speed the game is giving promotions - it shouldn't be too fast (or too slow).
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