How are abilities that contain multiple separate abilities like Living Language, Craft, and Area Lore handled? Do the Affinity (Ability) and Puissant (Ability) virtues apply to all the subcategories of one of these abilities, or only one subcategory? For example, would you take Affinity Living Language or Affinity French Language?
These actually regroup a number of different abilities under one entry in the book. So French and German are two completely different abilities, as are Craft: Baskets and Craft: Weaver.
So it would be Affinity with French, not Affinity with all Living Languages (but check out the Linguist Virtue in HoH:TL p.25). And Puissant Craft: Baskets, not Puissant Crafts.
Thanks! Linguist certainly looks interesting as it covers dead languages as well.
And in reading through the latest Sub Rosa, one of the authors uses the Linguist virtue as a template for other ability-based virtues. So, if your GM is amenable, you could have a "Crafter's Hands" virtue, which grants the quarter bonus to all Craft skills. But note that such a virtue would be a house rule, albeit one based pretty heavily on an existing virtue.
Or just go with Faerie Blood (Dwarf) which gives a +1 to all Crafts.
But I don't wanna be a dwarf!
Why? We could throw you so much farther if you were... 
Aye, and there's the rub.
I had meant to come back to this, in a serious post. I'm uncomfortable with a Linguist style of virtue for all crafts. However, I think it's wonderful on related crafts, such as various woodworking type of crafts getting the bonus, same with smithing. Weaving and sewing/tailoring. I'm not sure what other ability would fit with masonry, or if that's even considered a craft. 
Stoneworking, mining, and perhaps mountaineering (although this is more of a Profession).