I was happy to see the update, and I think this one has been my favorite, simply because of the focus on making the non-combat skills fun.
However, I understand and share your concern about using separate skill points or perks for combat vs. non-combat skills. That's a big part of the fun of leveling up for me, when there are number of different awesome options to choose from and I have to make a tough decision.
If we had a single pool of perk points for both, it would seem to be much more fun, or at least the replay value would be higher, as I'd be able to play very different character builds multiple times, focusing on any of a number of different skills, perhaps my first character might focus on piercing weapons and my second character might focus more on brewing poisons, for example.
I have never seen Sylvius be so wrong on an issue as this one...