I could certainly see that the computer might have a hard time figuring out what skill was appropriate, the suggestion (in terms of what it says about skill, and not how weapons are crafted) means to say that using weapons that are similar, based on the item type, default skill, and material should give bonuses to other things than the default skill itself. As with the sword example, if you train with one weapon for long enough you come to know the feel of the weapon and how to best use it, but you also become more skilled with weapons similar to it (being the item type) and then to a diminished extent all weapons that attack in a similar way (the way the current skill system works). I used to be an avid fencer, and while my experience taught me how to fight with my sword the best, it also taught me how to fight with rapiers in general, and one handed weapons, but the less a weapon is like a rapier, the less ability I have to use it well. In terms of dwarf fortress, a dwarf that uses one military issued weapon throughout his career, say a longsword, would be amazing with the weapon he was issued, great with longswords, good with swords, decent with one-handed weapons, decent with slashing weapons, but not great with a two-handed sword; he would be in the current system however.
One solution could be breaking the skill system down into smaller skills that will culminate into bigger effects, and perhaps having dynamically generated skills centered around very particular objects. This could break down into something that went from least specific to most specific this way Melee weapons-Bladed weapons-Swords-One Handed Swords-Scimitars-*steel scimitar*