I've pushed some additional updates to the master-ia/master-ia-patch branches. Notably, the formula that determines how much effort a slave puts into lessons or other tasks and how much merit they gain now gives less weight to fear, making mood and devotion (if you have it) more influential. A slave who is in a depressed mood (or who has despair in their aura) will often get F- grades. Max fear can compensate for this to an extent, but you'll need more than just fear to get a positive result; equipment bonuses, teaching bonuses (academy/tutor/master skill), etc. If you're not able to raise her mood, you might even consider using drugs, if you can make her take them...
This will be more noticeable on hardcore difficulty than normal difficulty, because on normal you will usually achieve positive obedience long before you reach 5 fear, and on normal difficulty, with positive obedience, even if the slave is depressed, she will still put at least minimal effort into whatever she does.
These adjustments seem to be working well from my testing so far, but I'll do a more extensive test tomorrow. Meanwhile, I'd appreciate feedback if anyone else wants to try it.