Hey just today I’ve been thinking of a similar thing. I wanted to have affinity be represented by number of skill points spent on creation (with a cap of 4), so that professions actually have some meaning, but your idea is better. It even allows for “forced professions” ie someone who learned to do something without actually liking that. The way professions are set up now there is virtually no difference between how a lumberjack and a computer hacker handle things, and very soon they both meld into the same mess of various skills whose books the character found.
Anyway, the main reason I’m posting is to mention some of my proposed tweaks - in my opinion raising skills through books at the moment is too easy, and to remedy that, we could have technical/boring books have higher morale penalties, as well as low focus factoring more into reducing skill gain from reading. (simulating being worn out after studying stuff that doesn’t particularly interest you). This morale penalty would be of course reduced (even to the point of becoming a bonus) for skills with high affinity. We could even have low affinity skills that would be trained slower and have higher morale penalties with reading.
There is also a power-playing idea: if you set the skill gain factor option to make skills X times slower to raise, the aptitudes could be exempt from this to some degree, to make characters be really differentiated in the late game. This factor of exemption could also be in the options (although this could possibly be overkill).
I like your take on skill rust, I hadn’t even thought of that.
The only issues I can see at the moment (which wouldn’t bother me personally) is whether and how to make affinity flexible, like Noctifer mentioned, and the question of whether most people would even like a different skill system, let alone one this elaborate.