The fatigue is one of the most annoying parts of SHIII. It's one area in which SH4 is a vast improvement (having a watch bill where your crew 'rotates' automatically is realistic and removes all the highly annoying moving of crew).
I find it so annoying and unrealistic that I always use 'no fatigue' via SH3 commander. Not realistic, either, but I find the issue of micro-managing my crew to be such an impediment I just couldn't be bothered with it. It's exaggerated further by the, in my opinion, unreasonably bad weather - your crew is fatigued more quickly when on the surface in bad weather.
Yes, you can change the fatigue cut in through SH3 commander (as has been explained). The trouble is your crew also won't recover from fatigue when you are at TC levels where fatigue doesn't accumulate, so you're on a downward slope once you start getting any fatigue.
As I said, I find it all so irritating I just disable fatigue. If it 'added' to the experience, or were better managed, I would leave it, but it isn't - so I don't!
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