Wow, you've picked one of the angrier topics on this forum to discuss. Beery is the one best qualified to talk about his fatigue system, and several others here are good at discussing other views on this subject. There are many recent threads on it in the MOD forum you should seek out.
As far as advice is concerned, no matter what fatigue system you use, or what you think of it, the best cure for fatigue in the game is medals. The more and better medals you give to your crew, the less they suffer from fatigue. Give medals to your officers first, as they have the most "power" to perform shipboard tasks, as well, they naturally resist fatigue better than the rest of the crew.
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