I am not quite sure if morevthan me would like it, and if it is realizable at all but here we go:
Mixed armour "monsters"
I have always deemed it a bit strange, that it should be of advantage, to wear a mixed armour set, because in reality this should result of adding up the weaknesses of each armour type.
Of course it is not the software, that favours this but the fact that you defend somewhat worse against the different types of weapons, but not as bad as the worst combination of weapon vs armour.
Now someone seeing a weakness in the opponents armour should usually go for those. (i.e. someone with a dagger will go for medium armor parts)
So maybe it would be worthwhile to decrease the attack probability against a strong armour part by half und double it against weak points.
Problem of that approach: it is fairly hard always to add up to 100% for the different parts
Easier to calculate would be to leave the probability the same, but decrease the protection of the weak or even all parts by some degree. Maybe 50% if only the weak parts are inflicted or 20% if all parts are affected.
Damage of arrows.
As far as I could determine the damage of distant weapons is calculated mostly by strength, while I believe it should be perception instead.
Another option might be, to increase the probability of critical hits with higher perception.
Perception in general
Would it be possible to limit how far a character can see by his perception? And have different distances for creatures and herbs? In Example with perception 20 you can view creatures at a base 10 + perception20/2 = 20 squares while someone nearly blind with perception 4 will see them only as far as 12 squares.
Similar for herbs with maybe a somewhat smaller base value.