There's more to it than what has already been mentioned. It may seem silly to award qualifications to all crew members, but that comes in very handy for me. Qualifications assigned by Commander to sailors do not affect their performance in game, but they can still be useful. I use them to add visual markers to my crew, so that I know where to assign them. I have two shifts of engine room, bridge watch, radio and helmsmen. When one group is fatigued, I swap them out one for one with fresh guys of the same qualification. You can also assign extra qualifications to officers, and they will help their efficiency in that department.
Commander varies the tonnage score for ships of the same type, allows you adjust your deck gun reload rate or do away entirely with your deck gun [a deckgun is moot at a certain point as planes and armed merchantmen make it impossible to use], time compression settings and many other factors. The fact that almost everybody here uses Commander should tell you something about its utility.
I also appreciate the realistic career length option. I could be retired at the end of a given patrol or get to go to sea one more time. This means each Kaleun will have only so many career patrols and results in more historical tonnage scores. I hate seeing a Kaleun with 800K of tonnage over 39 patrols, neither of which happened in real life. That alone adds uncertainty to my game, not knowing when I will be retired and causes me to try make the most out of each patrol. There are also options for sabotage and equipment breakdowns, as faced by real life Kaleuns. On one recent patrol my attack periscope malfunctioned; I was unable to zoom in my targets and had to make do with no magnification. That's fun, trying to ID your targets when they are tiny in your viewfinder. In addition to these, you have more options as to which crew fatigue model you wish to use, including no fatigue, realistic crew size configurations, limitation of boats available to you according to your flotillas as in real life, crew transfers or death of crewmen while on shore leave. How do think it would feel to find out your watch officer was killed by the French underground while on a train to Germany to visit his parents? All of this and more can happen to you if you explore all the feature of Commander.
Oh, almost forgot: Randomized crush depths for your sub and the simulation of thermal layers, something not modelled in the stock game. In spite of my detailed list, I am sure there are many other features I haven't covered, such as the choice of real German names compiled from the names of real U-boat men from WW2.
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