I've been struggling with fatigue rules that aren't just some lousy modifier to keep track of, and this is what I've come up with. I'm trying it currently in my game, and it seems to be working - it's simple to understand, and fairly severe in its implications.
When exhausted, lose all levels, and move as if fully encumbered. If already fully encumbered, you movement is at a shuffle (essentially 0 for overland travel).
Thus class skills are no longer accessible - Burglars can't free-run or climb, Magicians can't cast spells, Fighters get no attack/defense bonuses.
You're just a slow, normal human when exhausted.