Hi,
I must say I like the idea behind this mod/game. "Rusty" Fallout, survival etc.
That's why I've read this thread and the blog more carefully and I have some thought I'll share with you. As well as ideas - hopefully not all of them are rubbish
Regarding skill system changes
Unlike many previous posters, I don't mind them. I understand why it is a valid idea to merge the shooting skills in such game setting. No option is ever ideal, but imho the one you've chosen is the better one, as far as game balance is concerned. On other hand it is not essential.
Some said that energy weapons were common and available to civilians. But on other hand they weren't that common in Fallout games. And the energy cells were quite expensive and less common than other ammunition as well. Despite the in game descriptions, some energy weapons were made (or perhaps even designed) after the war, by BoS or others.
You may find some extra explanations why those weapons are so rare in the game area. EMP from the bombs would damage the electronics in energy weapons (the player could find such guns destroyed and unrepairable - even a lot of them in some location). The pre-war state could have imposed some laws prohibiting in some way civilians from buying such weapons. What was available before the war is probably not the best argument - think about the cars in Fallout setting. A lot of wrecks, but almost none working.
Another, quite funny scenario: the player finds such weapons and they are great, but the ammunition is totally unavailable so they are worthless (at least for most of the game).
I find merging H2H combat skills into one quite logical. Perhaps it wouldn't be in a medieval setting or a combat oriented game. Plus the player probably won't be using Power Fists etc. Actually knife combat isn't that far away from unarmed combat. You still have to control distance, maintain guard etc. I'm talking about basics, but learning the specifics isn't that difficult when you're already good at CQC.
I'd also consider merging Doctor and First Aid. Unless Doctor won't be redundant in your mod (healing diseases, for example).
You can add extra perks allowing for more specialization. For example a perk giving a bonus to melee weapons or energy weapons.
I can't agree with the "dumbing down" argument. In some cases reducing skill variety is bad, in some it is not. The skill system has to be tailored for the game/setting, not the other way around. Merging weapons skills into one would be bad in normal Fallout, but may be completely valid in this case.
From game mechanics and real life point of view, shooting from a laser gun isn't all that different than shooting from a normal gun. It's actually easier. There are lot of things that the shooter has to consider when using a normal firearm (recoil for example) that are different with energy weapons. But at close distance this may make no difference. A good small gun expert would probably be quite good with energy weapons after some basic training, but that's not the case in S.P.E.C.I.A.L.
Also, shooting from a sniper rifle is totally different than bursting from a SMG and probably a plasma rifle would require different technique than a laser rifle. But making 10 different and totally separate gun skills would make no sense.
Regarding aimed-shots and other combat mechanics
Shooting opponents in they eyes is a part of Fallout combat and it doesn't bother me at all. That said I don't mind your changes. And I agree that it was too easy (especially in Fallout 1) and oversimplified combat tactics.
I'd implement this change differently, though. Instead of removing eye-shots, I'd make them a lot harder. So even a well trained sniper would have a small chance to succeed. And I'd made the bonus even bigger. A nod towards risk-takers.
I don't know the Fallout Online engine, but I'd add a small AP cost for changing the weapon. In Fallout one could have a minigun in one slot, a plasma rifle in another and cycle them at no cost. If he had to spent 1 AP to do it, combat tactics would gain a new element for the player to consider. It could be annoying to some players though.
I'd also increase the AC bonus for unused AP points. Normally you get 1 AC for each AP left, which IIRC decreases enemies chance to hit by 1%. Not much given that you spend those APs on dodging and generally making live a lot harder for enemies to hit you.
2 AC for 1 AP with a perk increasing it to 3 AC for each AP would be good imho. Assuming that FO engine didn't change normal AP and AC figures.
If you have control of shooting modes, you could add a new one: long shot. The player spends more AP (maybe even twice as much) to aim carefully. This gives him a decent bonus to accuracy and a small bonus to critical chance. In some situations it would be better to fire once with a bigger chance to hit than fire twice with a smaller one. Some extra tactical options. But if it's hard to implement, there's no sense to spend time on it.
Regarding weapons:
I understand that guns and ammunition will be harder to get. With this in mind I'd suggest:
- Rebalancing small guns a bit. Make the gap between handguns and rifles more noticeable. This doesn't mean that all rifles must be powerful or that unrealistically powerful handguns can't exist
- Making special ammunition (JHP and AP for rifles) much rarer but also powerful. For example you may find only 3 AP rounds for your sniper rifle during the entire game, but they are very good.
It's a bit harder for handguns, because AFAIK expanding ammunition is used as often as the ball one (not AP! this implies a hard metal core). But this problem can be easily solved.
- At some point of the game a bow or crossbow could be used by the player or by some tribals
- Make the ammo for the best guns generally rare (or even very rare). This way player won't be able to shoot to every enemy with his Sniper Rifle. He'd had to use a weaker gun most of the time, and the rifle only against stronger opponents. Cycling between guns during one shootout would be even more important.
- I'd increase the chance of a critical failure resulting in gun stoppage or a misfire. Maybe not those resulting in damage to the weapon, because it will be too irritating for the players.
Ammo could be also crafted by the player
Shells could be found on dead enemies (with guns), gunpowder made with chemicals (science) etc. Or at least he could sell the shells.
An interesting idea would be to allow the player to find great energy weapons at some military stash, even early in the game. But there would be no ammo available for them
Actually energy guns could be quite common at that stage of the timeline, but without ammo or damaged beyond repair (with resources available for the player/NPCs). A small twist for the setting.
Imagine a special random encounter with a old battle ground, full of bodies of soldiers in destroyed combat / power armour and with totally useless high tech guns
I don't know if the FO engine supports item wear/damage. If it does, be very careful with it. I personally find the system in Fallout 3 annoying. Repairing weapons with other weapons even if the damage isn't big is also a bit stupid.
A good gun shouldn't damage itself with each shot, assuming that the owner takes care of it. I'd allow the player to clean \the gun to repair some damage, but only if the gun is in good shape. For example a weapon with 100% durability before a fight has 90% after it. The player can clean it to regain the 100%. But if it gets damaged to 70% after a critical failure, cleaning wont work at all. I hope you understand what I mean.
Of course weapons found by the player may be damage and require repairs or spare parts.
If no wear system is present, you can probably emulate it. Just create two or three versions of weapons (when needed): fully functional, worn and damaged. The damaged doesn't work, worn has a bit less damage and smaller range. Maybe is less reliable.
This way the player may find weapons in various shape and repair them (or pay NPCs for it). They can get damaged after a bad critical failure.
Regarding other things:
I'd made skill books a less common. Not too much, but this way you will encourage the player to spent skill points on skills which he would normally increase only by reading books.
But add some special/unique boosk. For example a Vault-Tec Nuclear War Survival Guide increasing Survival but also Science, Repair and Doctor by a small amount.
If you plan to force the player to eat like in ADOM, be careful with it. Usually such features turn out to be mighty annoying. Survival skill could probably deal with this problem (increasing or decreasing the chance of "no food" or "no water" encounters).
Diseases could be a nice addition to the game. As a background thing (people lacking medication etc.) and maybe to some extend as something that can affect the player.
You wrote that the fights will be quite rare. Watch out to not overdo, because many players enjoy combat in Fallout as much as the setting, plot and quests.
Make Rad-X less effective or less common and radiation more common. This way the player will have to deal with it more often. It would also make perks like rad resistant more useful. This requires balancing.
Good luck.
And no, it wasn't because of the "questionable Skill treatment" issue. 
Your mod sounds great; I'm looking forward to trying it out. :=)
I had to think about that one for a moment. Much funnier (and more euphamistic) than "condoms."