I've discussed this outside the forums, but I'm glad to see someone else is interested in this idea!
I know people constantly bounce of this idea of "balance", but I think having negatives on our gear will help enforce that idea of true balance.
+1

I feel the concept behind the sets is to weigh up their defensive capabilities against the bonuses they grant you. As opposed to throwing positives and negatives, they just offer positives, and the negatives are derived from there being no positive.

As in, take the Vog Cub set you mentioned. It offers no piercing defense, so you'll naturally take more damage from beasts over if you were wearing the Skolver set. In saying that, you'd sustain less damage from a construct's attack in Vog Cub than you would in Skolver. I'd probably the difference isn't terribly big, so there is an issue there; but determining what penalty should be applied is a bit.. awkward. If Vog takes more damage from beasts, what does Skolver and Snarbolax have wrong with it?

Now, here's a technical issue with family-based attacks. At a guess, it's implemented that families derive their "attack type" from a set, ie. normal, piercing, etc. Although they cross over, for family-based defense penalties to work, if you take damage, it needs to determine the family of the attack as opposed to the type. So you essentially have two systems working next to each other, which is a complete waste of time from a technical point-of-view. A technical fix would be to have families use a family-based damage type, and apply that to a set of the original damage types (which, I'd assume, monster defense types work similar to - but that's a different system entirely).

Overall, penalties might be a good way to try and balance out sets, but I don't feel family-based defense penalties are the way to go.