Those ideas are good and interesting.
A bit more detailed reply:
Morale: Based on the outcome of a JA2-esque personality evaluation, it is decided how much the player's morale is impaired by things like killing people (especially children) and getting hurt, and how much it is improved by things like alcohol and good deeds. Any eventual morale failure lasts one turn and impacts either moving speed or to hit chances or attack AP cost (the reason is that where NPC's are regular humans who panic from time to time, the player has the unfair advantage of being something of a B-Movie action hero).
Good as long as personality system is going to be reasonably comprehensive. Otherwise it's better to be a B-Movie action hero than to be arbitrarily barred from having particular personality traits.
Consistent Localization: Now, if you have, say, a 25% chance of hitting someone when aiming for the eye, this means you have a 25% chance of hitting the target, so also the head or body (because it's very strange that narrowly missing someone's eyes doesn't result in you hitting the head)
I don't quite get what you're trying to say.
On one hand, yes, missing particular location should involve checking if you haven't hit adjacent location, but on the other there are pretty good reasons why professionals tend to aim for center mass when trying to shoot someone - aiming at peripheral body parts should make it more likely to miss.
Overall you'd need some sort of structure telling the game which body parts are adjacent to one another and which are in peripheral locations as well as ability to convert difference between roll's difficulty and result into meaningful measure of how much did you miss and using this information to calculate new to-hit difficulty for hitting particular body parts.
You could visualize it as finding radius of a circle circumscribed around targetted body part and then finding percentages of circle's circumference intersecting individual body parts. Of course, since fallout doesn't have the sort of spatial information, you'd have to come up with the math by yourself - I don't even know how FO calculates to-hit difficulty.
No More AC: Dodging an attack now depends on your agility and perks, and actually becomes harder the more bulky armor you wear (because AC is a weird schizophrenic stat in Fallout which seems to embody both attacks ricocheting off armor and you nimbly dodging them; better to split it up into agility and DT/DR).
I gather it tries to incorporate glancing hits as well as dodging, DT and DR, but it doesn't quite work. I'd replace AC by dodge and add "attack angle modifier" of sorts, increasing DT and DR based on the difference between actual and perfect roll value for successful shot divided by the difference between threshold and perfect value of the roll (to compensate for other modifiers such as distance - you need to know how much off-center you hit the actual target).
Critical Failures Can Always Happen/100% To Hit Cap: Even a "hit" can turn into a critical miss if you first fail a skill roll and then a luck roll. As a consequence the max to hit is raised from 95 to 100 percent. (because it was strange that your weapon could only spontaneously explode if you were already going to miss, and the arbitrary 95% cap was only meant to accommodate this weird system)
A hunderd times this. Criticals system was a stinking mess in FO.
Critical failure chance, at least for ranged attacks should be completely independent of difficulty of the attack, it should be entirely determined by attacker's skill, attributes and status, plus possibly modifiers from weapon itself.
Just because you're trying to hit a running dude in the eye at night, in the rain from km away doesn't make it any more likely that you'll drop your ammo while simultaneously shooting yourself in both feet. It just means that you will likely miss.
Increasing Reloading/Inventory AP Cost: Because reloading a minigun should take longer than it takes to take two steps.
The optimal way would be splitting shooting into lengthier target acquisition (based on amount of hex sides to turn and slightly on distance, as well as weapon) and very fast and cheap shooting. You should be able to acquire empty hexes as well (so, you know guy is going to appear from behind the corner of a building, you aim at this corner), and "stick" it to even moving traget, both when aiming at empty space and something passes through and when aiming at actual target - you can visualize aiming at empty space as laying a "trap" of sorts that get triggered by anyone passing through and sticks crosshairs on them.
Reloading should indeed take the longest.
I have proposed such a system here previously.
Stimpak Changes: (Super-)Stimpaks now mainly serve to heal temporary damage, though super Stimpaks also raise the max HP temporarily (because it never made sense that you could survive a hundred consecutive shots to the head in a single battle merely by injecting a liquid in the wounds repeatedly).
Definitely. Stimpaks should be only temporary HP boost and wear off completely over time.
Healing Rate as First Aid Dependent: If you "rest", your healing rate goes up depending on your First Aid skill (I never bought that you could sleep off bullet wounds, and given that the active First Aid skill works like shit, might as well make resting into a medical break).
How about restricting healing by resting to only minor wounds?
I'd modify healing rate based on HP percentage (unmodified, so any transient effects like stimpacks are removed prior to calculation) - if it's above certain (presumably rather high) threshold you heal faster the further you are from it. If it's below the same or different threshold, your health deteriorates faster the further away you're from it.
So, you don't get to heal anything but light damage by just sleeping it over. You might need to give more NPCs medical skills, though.
Maybe merge medical skills too.
Skill Books: The idea that your Sledgehammer-wielding retard character would spend weeks on end studying science books to end the game with a Science skill higher than most physics teachers was always stupid, so I want to make skill books unusable reference material that raises your skill as you carry them around.
I think you should have stat and skill thresholds for book usability. Too low and they are incomprehensible babble to you, to high and you already know that.
If you go through with "reference material" idea, then maybe make it so that the bonus decreases as you use skill with book in your inventory, but your skill increases by the same amount, representing the knowledge you use rubbing off on you.
Also, gun rags should definitely be exempt for that rule (because you're not going to use them as reference in combat), but some instance ID mechanics could be used to tag individual instances as read, but prevent your character from just eating them.