I would second the vote for SH3 Commander.
It is very easy to use and will let you adjust the things people most commonly want to change about the game (water clarity, time compression, gun reload rates, hull integrity indicator, fatigue model etc.) to your personal taste. It automatically provides some neat features not normally present in the game, like variable crush depths and thermal layers. It also has a lot of neat options for where and in what type of sub to start your career, number of days to spend in base etc. (and this just scratches the surface of what you can do with it). Heartily recommended.
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