(Most of these impressions are from 0.73)

Maybe it's different for other players, but a lot of enemies seem to be both hard to hit or damage, and also have a hard time hitting or damaging me. I was playing a vigilante using a Xul katana and an energy shield, so maybe I was too weak and defensive, but from my impression everyone could stand to hit and deal damage more consistently.. Bandit spellcasters were very dangerous because they did lots of damage from a distance on occasion; the only comparable melee enemies were Kin Blademasters.

I would up leaning heavily on damage spells just because they reliably did damage with every cast. Juke, and later charge, often did no damage and seemed like a waste of stamina except for when I really needed the stun effect. Similarly bandit spellcasters were very dangerous for their damage but enemies with Juke weren't very threatening. The only comparable melee enemies I found were Kin Blademasters.

Another possibility is that I'm supposed to be super-duper mutated and achieve massive power that way, but I've yet to experiment with that. Radiation sounds bad in the abstract, and the existence of iodine pills suggests that I may want to avoid mutating entirely.

Ranged weapons seemed weak too, although I didn't develop the skill and it's possible that they're powerful with practice. I ended up accumulating hundreds of bullets, and I was really reluctant to shoot them all just to gain the skill.

A related concern is that the weapon damage dice don't seem to match up to their actual performance, so I'm not sure how to interpret them. At one point I had lucked into having an unusually powerful 3d1+2 (IIRC) freezing scalpel, and when it hit it would consistently deal ~10-12 damage instead of the expected 5 damage every time. I bought a greatsword for comparison, and it did less damage very consistently despite appearing to have better dice. It didn't seem like the scalpel was supposed to be an amazing item, because I found in it the first dungeon and it was only worth <$30 to a merchant.

Despite all this, I really like your game and I played both main factions' questlines as far as I could. Keep up the great work!

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.