Just a thought about this system that seems to get people upset. As it is now when you hit fatigue you get less skill points for your job. What if instead of fatigue you had an skill bonus to start out with , then when that ran out (i.e. you hit fatigue) you get normal skill point gains? It's all a bit of semantics ,but I've played other mmo's with a system like that where you get an initial bonus to experience but after some time playing it returns to normal experience.
Anyway perhaps by rewording the way fatigue works is all it needs to satisfy those who believe they are being punished by fatigue. When in fact they are being rewarded initially with bonus skill points!