As far as affinities, I believe if each skill should have a Favorable Class (The class that its learned from) And Cross Class (Skill from a different class) Designation.
But then also a Core Job (Job that focuses around this skill) Favorable Job (Job that can use this skill) Neutral Job (Job that is neither for or against the skill) and an Opposing Job (Job that normally can not use the skill)
Each of those statuses give a point.
Favored Class: 2
Cross Class: 1
Core Job: 3
Favored Job: 2
Neutral Job: 1
Opposing Job: -3
As an Example we'll use Conjurer / White Mage with the Skill Cure.
Conjurer for Cure is a Favored Class: it earns 2 Points
White Mage for Cure is a Core Job: it earns 3 points.
Total 5 Points:
Each point gives 20% Affinity: so Conjurer / White Mage can use Cure at 100% Affinity.
Then we take a look at.
Pugilist / Monk:
Pugilist is Cross Class for Cure: 1
Monk is Neutral for Cure: 1
Total is 2 Points:
Pugilist / Monk can use cure at 40% Affinity.
Now. If the Pugilist equips a Conjurers Affinity trait, he can push it to 50%.
Now we'll take a look at.
Thaumaturge / Black Mage:
Thaumaturge is a Cross Class for Cure : 1
Black Mage is an Opposing Job for Cure: -3
Total Points -2
Because you have to have positive affinity to equip the skill, and -2 points means -40% affinity.
Black Mage Can Not Equip Cure.