The fundamental problem with the current AR/AP system is that there is a very small window in which penetration is by far the most valuable stat available. And outside that window it does either literally nothing or virtually nothing.
For example, take an opponent with 15 armor.
The first 12 points of penetration do literally nothing.
The next 1 point is a 100% damage increase.
The next 1 point is a further 50% damage increase.
The next 1 point is a further 33% damage increase.
After that, the next 15 points are about a 2% damage increase each.
The way the maths works out is that points 13-15 of penetration generate a total 300% damage increase, and the rest do practically nothing. Trying to fix this by giving NPCs more/less armor/penetration just shifts the window of opportunity, it doesn't fix the problem. There's never going to be a good way to balance a system that has such a tiny window of effectiveness.
(Incidentally, due to the ridiculous double inversion maths actually used in the game, the problem is actually slightly worse in practice than in the example above. But the maths for that gets very complicated and the problem is still the same)
The system needs to be redesigned such that armor and penetration have a much bigger window of effectiveness. Perhaps something like 1 armor = 5% damage reduction (capped at say 75%), and that each point of penetration reduces that damage reduction by 5%. So with say 10 armor that would be 50% damage reduction but 10 penetration would reduce that reduction by 50% (i.e. a net 25% damage reduction).
It would mean that penetration gains increasing value as your opponent has more armor (which feels right to me), but both will always be useful to have.