How about: each class has associated with it a set of stats which are combined to achieve the current effect of wisdom and a different set of stats which are combined to achieve the current effect of intelligence, for the purpose of practices and learning.

Then, for skills which are shared common to a number of classes tie them to a particular class. For example, sword is a warrior skill, pen is a bard skill. For these skills, use a ratio to determine the benefit of practices (warrior practicing pen gets his practice benefit multiplied by his "bard wisdom" and "bard intelligence" and divided by his "warrior wisdom" and "warrior intelligence").

This should achieve something similar to what you were proposing, but I think it's a lot simpler: Instead of coming up with stats for each skill, you're coming up with stats for each class, and classes for each skill.