050 did not have scars. CVS did.

I have an idea. Input/expansion would be nice... All numbers are totally made up and would be subject to balance, of course.

Generation: Scars are not received immediately on injury; instead, they occur during the healing process. Each time you recover a hit point, there is a very small chance you will be scarred. This chance is increased by the following conditions:
* Lower HP in that limb (before the healing happens) increases the chance linearly. So, healing from a single serious injury is more likely to cause scarring than from many small injuries. Perhaps the scale goes like 3x chance at 50% limb health, linearly in-between.
* Regenerative effects (NOT magical healing, but something like fast-healing) incur an additional 1.5x multiplier to the scar probability
* Reattaching a severed limb has a 10% chance to scar the limb and the attachment point (i.e. torso). Each scar is rolled separately, so you may end up with two scars.
* Having an attached limb of an artificial material increases scar probability by 1.5x.
So, two example cases. For the sake of argument, let's say the base scar chance is 0.25%. You take a 1-point blow to your 2-hp head. When you heal that 1 hp of damage, there is a 0.75% chance you will gain a facial scar. If you drink some trolls blood, this increases to (0.75)*1.5=1.125% chance of a scar. Now, let's say your 10 hp torso took a 5-point blow. You have two fancy arcanite arms. So, recovering to 6 torso hp with trolls blood has a (0.75)*1.5*1.5*1.5=2.53125% chance of giving you a scar. Healing to full will scar your torso about 7.3% of the time. Healing naturally with no artificial limbs reduces this to about 2.2%.
* Scabies (or, more rarely, Cruentus or Mortifer) will sometimes inflict (or gift?) scars.

Effects: Scars have three effects. The first is dependent on location.
* Scars to the arms incur a small dexterity penalty. Something like -0.25 per scar. (Scars do make movement harder.)
* Scars to the legs incur a small agility penalty. Comparable to the arm penalty.
* Scars to the torso and groin inflict a small max HP penalty. I'm thinking -0.5 per scar. (You took a serious wound, and the injury might be permanent.)
The second is not:
* Each exposed (not covered) scar inflicts a modest Charisma penalty; facial scars count double. Gloves cover the arms, boots cover the legs, armor covers the body and groin. Cloaks count half for every body part (i.e. they half the penalty). Normal helmets cover 1/4 the head. Full helmets cover 1/3 of the head. Helmets of Attractivity completely cover the head. (Nobody really wants to look at your scarred face.)
* To offset this, charisma training is increased proportionally to either the root or the log of the number of exposed scars; again, facial scars count double. (You learn to use your scars to your advantage.)
* To offset the HP penalty, a similar (but smaller) bonus to endurance training applies with the total number of scars, covered or not. (Getting slashed with a sword isn't quite as scary after you take a spear through your gut.)
* Each scar counts as a point of Wisdom, for the purposes of piety gain with Scabies. A similar bonus applies for Cruentus and Mortifer, but reduced.
There is no offset to the dexterity or agility penalties. They're small. You'll just have to live with them.

Removal: If you are at full HP, with no missing limbs, healing liquid (or other magical healing effects, such as Seges) have a chance to remove a random scar. The check should run multiple times, so that a full bottle of healing liquid might be expected to heal 2-4 scars. Priests at altars might also remove scars. Removing scars will upset Scabies.

If it's handled on a "took minimum percent damage", be aware that virtually every blow to the head will result in a scar.

Sometimes, lighting is remembered when you move away from a tile, resulting in an almost-completely-black spot in an explored part of map. Mostly seems to happen with walls.

I feel I must point out that any opinions I make about the current state of the game are uninformed. I haven't played this version, and I didn't play the last version much either. That said, I don't think that magic, or psychic powers, really correlates well with size. If it did, polar bears would be far more intimidating.

A regular worm, sure. But these are mind worms. Clearly they have mental abilities unknown to mere humans.

Nothing should be stronger than Valpurium.

The idea of some materials having properties other than flexibility, hardness, and luminosity is great. I don't know the state of the current code, but that might be hard. It's certainly impossible with script coding only.

As for psypher itself: Assuming unique material properties are possible, perhaps psypher has a middle-high hardness and low (but not awful) flexibility, with the hidden property of abusing int and wis based on quantity (volume) and proximity (inverse square)... And perhaps it has a relatively low Int requirement. The result is that it becomes a good mid level material which stunts your long term development.

I already make use of thrown weapons. Spare light-weight weapons (daggers, spears, axes, or hammers - depends on which primary weapon skill I'm training) go into my inventory and thrown at enemies before I engage them. Trains the weapon skill and lets me hurt them at a distance. Requires a lot of micromanagement though...

Maybe some alternative super-hard semi-optional room with level-wide implications?

It's really difficult to compare IVAN and DCSS. DCSS has a lot of excellent ideas in it, which a lot of other games could learn from... but adding some of these ideas would make IVAN feel like DCSS with limbs.

That being said: If you are interested, and get the coding skill, you could probably write a DCSS-esque fork! A lot of people have made excellent forks of IVAN, with all sorts of interesting additions and changes. Most of them don't play with the mechanics, but as long as you're doing the coding you're free to do what you like!

Have you considered reworking unarmed combat? Currently if you have arms you punch, if you don't have arms you kick, if you have neither arms nor legs you bite. (Barring vampire.) If a person wearing Boots of Kicking preferentially kicked in melee, or if the actual attack performed depended on relative skill levels, it might make the boots of kicking more useful.

Another model might be to take a page from Crawl: if the limb is free, you have a (skill)/(skill+X) chance of attacking with the limb whenever you make a normal melee attack. X can be tuned for balance. Allows a skilled boxer who picks up a knife to keep punching between stabs, or someone who is good at kicking to get free kicks once in a while. X could include a constant, modifiers from e.g. encumbrance, and even be reduced by stats. How many free attacks per round of melee are possible would be a different discussion: should a highly skilled boxer, kicker, and biter be able to stab with a sword, punch, kick, and bite all in one round? Etc.