All the custom skills that are "not working" are only due to the fact that the skills aren't added to the AI. Technically it's feasible for modders to integrate those skills to AI. It's just a mod per mod case.

I see where your frustration comes from but it's not because of this mod but rather of the custom spells mods. On the same token those mods shouldn't be working on enemy characters then since AI isn't programmed for them.

Yeah, I actually played around with it more and found a couple of custom skills were working but, it was few and far between. The first playthrough, I made the AI character use Tracker Skills from a mod and she would only use a basic attack. Switched her to fairy and she did plenty.

It's most likely how the skills were made. In the Fairy case they probably re-used existing skills with an AI with high enough priority already existing and just tweaked the skills to make them unique instead of making them entirely new.

And of course the entire mod isn't perfect because it relies on AI, I've played quite a bit with only AI as allies and they sometimes have weird tactics. They tend to prioritize damaging undead over healing and defense over offense in the majority of cases and overall Polymorph don't seem to be very compatible either for spells that have to be first toggled to get a new body part.

Likewise Summoners have a weird extremly high priority on totem summoning so that any ally with the summoning totem spell will essentially always use 2 AP per turn to summon a totme. Which can be amazing for a totem based character but extremly annoying in many other cases.