Look to AD&D. Look to real life.
And use logic.
One of my projects, that's very rooted in old school AD&D has:
Crushing, Slashing, Piercing, Cleaving and Armor Piercing as elements. Along with quite a few others that aren't pertinent.
Armors have different rates for all of them. For example: Full Plate has 70% vs Slashing, 90% vs Crushing, 75% vs piercing, no reduction against cleaving, and 120% vs armor piercing. In addition to adding Def.
Leather and other soft armors give better protection from crushing damage, but don't reduce against anything else. They just add Def.
There is also an 'Enchanted' element, which all non-enchanted armor is weak against.
Armor also reduces magic and agility.
Using a plug-in I can give every weapon a base physical element, then add others, and have them all proc.
Cleaving is for weapons like pole-arms. They tend to do high damage, and most things don't get much, if any, protection from them, but they're slow.
For enemies I just consider their bodies. A skeleton wont care about arrows and spears, so they get a high reduction to piercing damage. They do break easy, so crushing does plenty of damage.
Zombies don't really care what you do to their flesh, unless you cut it off... so piercing and crushing do very little damage, while slashing does a lot.
Ethereal enemies, like ghosts, have a decent to high flat reduction of all physical damage types. After all, they don't have much (if any) physical form to hit. It's either magic weapons/spells or RUN AWAY!
If they're in armor, I give them the same reductions, if any, from that type of armor. Same for any weapons they may have. I intend that enemies will drop all their gear, so I already have everything in the weapon/armor/skill database. I just give the baddie whatever the player would get from it.
Most of the time it wont matter.
As for the rest, keep it logical and most people should figure it out easily enough. And if they don't... well, you can't account for everyone.