Really great summaries. I agree with your analysis and conclusions.
I feel that the first step is going to be adding skill point requirements for ability use.
Once that is done, the defensive stats needs to be tweaked, I like the scaling flat bonus and percentage bonus suggested earlier, with some tweaks to the numbers of course.

My individual suggestions for skills.
Dual wield - remove critical chance, increase damage to 4%.
Single handed, increase accuracy to 3%
two hand - remove critical damage component.

Then have all skills slightly increase effectiveness for the abilities that fall under those skill points. Though I have a hard time imagining exactly what this last step would look like.

Outliers, geo should have a greater increase to poison damage.
Warfare could absorb the critical damage bonus from 2h instead of bonus damage to physical armor.
In the same vein, aerotheurge should increase spell critical chance (huh?)
Oh yeah, spells should just have critical hits and savage sortilege should be removed