On vacation at the moment, so my reply can't be as thorough as I would like.
I agree that there is a very large difference in reliability between standard attacks and abilities. I'm still unsure on how to deal with this. I know some should increase in power faster, particularly ones that use your weapon to attack, like juke and charge. Enemies seem to be able to take more hits and hit more reliably is due to their stats being more fixed than the player. The damage calculations are identical, though each NPC has it's own accuracy and weapon skill level. Later on in the game, these numbers increase quite a bit. Mutations, especially ones that grant extra limbs, are the "intended" progression path. This, combined with more powerful synthetic limbs can easily make the game a joke. The iodine pills and genetic stabilizers are simply one option for players, not something you need to use.
Weapon damage takes into account your character's strength and weapon skill into account when rolling for damage. The die roll is additive on top. This is why you are dealing more damage than anticipated. It is then reduced by the target's armor on the hit limb. (Which, in the case of NPCs, is generally the same for all body parts for now) Scalpels have the benefit of being very fast with more consistent damage. I think I need to do another balance pass where some weapons rely more on other stats. Strength wouldn't be too useful when wielding a smaller weapon.