I like that idea. I often give my 2014 monsters feats, which is something I will continue to do with the 2024 monsters, so why not give those proficient with weapons the corresponding weapon masteries as well?
As for skeletons, I reckon they should be resistant to piercing weapons. Stabbing a skeleton just doesn't seem like it would be all that effective. I like the idea that piercing weapons are ineffective, slashing weapons are OK, and bludgeoning weapons are the best.
Correspondingly, perhaps zombies should be vulnerable to slashing damage and resistant to piercing and bludgeoning.
I reckon this kind of stuff makes for more diverse combats too, as players will want to have a variety of weapons and switch between them depending on what they are fighting.