OK. This is my take at a revised fatigue system. It's based on the RQ III system but I've "imporoved" it. You may not agree of course...

Comments are welcome - as always.
Fatigue
All characters have a fatigue point pool equal to the sum of the characters STR and CON. Doing things that makes you tired, such as running, swimming, fighting and climbing, reduces the available fatigue points. Each melee round of hard work (running, hasty swimming or swimming in rough sea, etc.) reduces the FP pool by 2 points. Each melee round of medium work (fighting, swimming, climbing, riding at full speed, etc.) reduces the FP pool by one point. Wearing stuff also reduces the FP pool.
When a character carries stuff the sum of the ENC values of the tings carried are deducted from the fatigue point pool. However the ENC value reflects how cumbersome it would be to carry a thing in ones arms or on the back. Some items, most notable armour, do not encumber as much when worn as when carried on the back. The ENC of armour is halved (round up) when worn. An option would of course be to recalculate all armour ENC and rule that when not worn a piece of armours ENC is doubled.
When a characters FP pool reaches zero (0) the character becomes fatigued. Every new FP lost reduces all skills by 1 percentile. A fatigued character may not run or do any other hard work. He may fight, cast spells and ride at normal speed, etc. When a characters FP pool is so depleted that it has reached (0 – (STR + CON)) or less the character becomes exhausted. The character must make a CON x 5 (-FP) roll or collapse, if the character succeeds he may still do nothing but walk. Any physical activities (including casting spells) requires another CON x 5 (-FP) roll or the character collapses. If a character drives his FP pool below (0 – (STR + CON + CON)) he may die as a result of the strain. The character must succeed with a CON x 5 (-FP) roll or he dies…
A suggestion to simplify play: only count negative FP in chunks of 5. That is if a character has -6 FP, give her only -5 in all skills until she drops below -10. This will lessen the bookkeeping burden somewhat.
A character that falls unconscious because his HP total drops below 2 hp looses all positive FP (his FP pool drops to zero). Failing a shock roll, loosing all HP in the head or having a limb severed (i.e. the limbs take twice the normal hp value in total damage) also reduces FP to zero.
A character recovers FP at a rate equal to CON /2 rounded up per 5 melee rounds (i.e. per minute). The average character with CON 11 and a FP of 22 thus recovers in slightly more than four minutes. As an other example, a very well trained Dwarf character with STR 16 and CON 22, fully recovers in slightly less than four minutes.
It would seem that all character would fully recover in about four minutes. Only characters that are relatively speaking weak but has high cardio (CON) fully recovers faster. But very fit characters manages to recover more FP in a given time frame, which might be crucial in some circumstances.
/Peter