80% of the valid problems being raised with the new system (which I still think is a huge step in the right direction overall) might be solved by something like this:
Investing ability points in skills should yield more benefits than just increasing the number of skills available (at this point this benefit seems irrelevant - having more than 3 spells per school is not necessary). A higher skill level should unlock more powerful skills, improve skills and/or reduce AP costs. So, if the new system is retained, skills should also be given a skill level pre-requisite in addition to the character level and/or attribute pre-requisites.
In other words, it'd be a partial retread of the previous beta versions' system, with skills divided by ability level prereqs into "Level 1" through "Level 5" skills, while character level and/or attributes would make the skills stronger and/or act as additional prerequisites.
I also agree with the below feedback on ability naming/grouping:
I like the reorganization of the abilities into their new categories (although I'm not sure why Barter is under the "Craftsmanship" instead of "Personality").
I don't like that the names of the skills are different than the names of the abilities. Air, Earth, Water, Fire, Witchcraft, ... Ranger, etc. makes sense. Different name doesn't make it any cooler and just add more complexity.
Finally, I really like how the old "Way of..." ability bonuses were divided into the bonuses given by the "skill" abilities and other more general bonuses given by talents. That said, I think many of the talents are still too tied to these new skills in ways that prevent broader character customization, or that simply don't make sense. The worst offenders for these talents:
1) "Headstrong" (20% bonus against Frozen/Stunned/Petrified/Knocked Down) - prereq should be Constitution or Willpower, not "Scoundrel" ability
2) "Sidewinder" (decreases flanking penalty) - prereq should be Speed or some other stat, not "Man-at-Arms" ability
3) "Thick Skin" (extra armor) - benefit calculation should scale on Constitution, Body Building, or Armour Specialist, not on "Man-at-Arms" ability
4) "Weather the Storm" (extra magic resistance) - prereq and benefit calculation should be/scale on Willpower, not "Man-at-Arms" ability