They are two totally different tools which have nothing to do with each other. They can and should both be used.
SH3Gen generates war reports and assigns missions, showing more or less ships in port based on 'spy reports', and adjustable as to amount and reliablility.
SH3 Commander generates millions of possible crew names; lets you award more medals to the crew; lets you adjust several parameters including gun reload times, wave height, days in base as well as time compression settings; assigns names to the ships you sink, generates patrol reports which compare your scores to those of real commanders at that time; lets you select 'surrendered' as an option when you are killed; lets you select 'realistic career length', which retires you; takes away crew members (anything from 'transferred' to 'killed in bar fight'); and does a whole bunch of other stuff as well.
As far as I'm concerned, Commander is more important than even the best mods.
Yes, get them both.
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