I'm still tinkering with my list of suggestions for overhauling the body structure when the Combat Arc begins.
For body structure, I think a slightly more complicated system can be afforded.
Several systems, in fact.
First is attack size. An arrow is, naturally, a very direct attack. It cannot damage more that one-two organs of a human-sized creature. Now consider an arrow hitting a pixie. It'll be an equivalent of a ballista bolt, the poor thing will be ripped apart. So, make attack effects apply basing on size difference between attack and the creature.
Second is organ size. Without resorting to mapping all parts/organs on a 3d matrix, the best we can hope to achieve is have organs have a facing relative to the body and relative size. Have six tags for facing (front/rear/up/low/left/right), and organ size is basically the chance that an organ will be hit by any given attack.
Third is attack propagation. Any part that receives damage should propagate that damage to the parts that are eligible for receiving that damage. An example is a skull or a ribcage - there's a chance the ribcage will be hit (a large chance) when the upper body is hit, and if the damage that is passed to the ribcage is critical (i.e. it will affect INTERNAL organs), the ribcage part propagates that damage to the parts it contains - the lungs and the heart, that have smaller individual hit chances.
Fourth is attack continuity and direction. When the size of the attack is sufficient in relation to the target, so that several connected large parts may (realistically) be damaged, attack propagation will continue in the direction of the attack, which is defined randomly, in accordance with attack type.
A piercing attack will extend effect on one axis, using facing tags to determine the parts it hit. (the spine is in the back, the liver is in the front, a spear can hit them both, but cannot hit a kidney at the same time if it already struck center)
A slashing attack will instead affect only the parts that are facing it, but it will also be able to hit perpendicularly aligned parts (i.e. left/right/up/low when attacking from the front), propagating damage even to unconnected parts if necessary, but not exceeding the damage ratio set by size difference. (both arms can be hit by one attack)
Bashing and magic attacks influence parent and child parts when propagating, without regard to facing. (a hit to the upper body can also break a shoulder or neck)
Fifth is metaparts. Metaparts are parts that are named, but do not exist within the body, save as a name for a collection of parts it houses. For example, the ever-present ribcage. The ribcage is a collection of ribs, more or less. If all ribs are broken, the ribcage is destroyed. However, currently it may be that the ribcage is mangled, but most ribs are whole. This is avoided by making the ribcage just a name for a container. It receives damage, but has no health - instead it uses damage propagation to have its components damaged.
Sixth is property profiles for parts. Each part can be assigned a profile, as in "resists slashing and piercing, damaged easily by bashing, does not bleed, does not cause pain, immune to injections" - that would be for a horn or any other hard bone part. These will allow precise control over which parts are vital and which are not. Also, damage propagation will be affected by the damage resists, where if an attack hits a resistant part, its damage and hit rating decreases, lowering the chance of hitting something that the part may be containing. This applies in sequence to all damaged parts - for example, in an upper body, first the ribcage would be hit by an arrow, and the ribs it has would be affected first, as they would be damaged without a critical check. Once the arrow applies its damage (to just one rib, most probably), the pierce resistance of bone will decrease the arrow's damage potential, and it may lower enough to avert the damage to vitals.
Seventh... uh. There's quite a lot of this stuff. There're lists of tags for different effects on parts, attacks, weapons, and stuff like that. Like tags for multiple attacks on one weapon, parsed message text, etc, etc.