It's fine if you don't like it, but it's not bad design. Different is not automatically bad.

You are correct that different is not automatically bad; however, the ways in which the different idea in question is executed do make it highly flawed. A game revolving around positioning is one thing, and it's one I can appreciate (and I do when it comes to SoC, once I get a hold of a gun that isn't overly impacted by stats), but when the positioning is necessitated in part by overly stat influenced inaccuracy, that's a major design flaw. The stat induced accuracy could have easily not been as big an issue if taking the time to mentally steel the character and line up a shot (like every sniper in existence on a good day) ensured tighter accuracy as opposed to always trying to simulate the aim of one who is constantly in a combat scenario where that degree of aiming is impossible, and if it had a reduced effect overall to account for player reflexes while still rendering certain weapons useless beyond certain ranges.

As it stands, constant forced inaccuracy of this kind is overly cumulative with inaccuracy resulting from the player and does not reflect what should happen in any given situation where the player has the advantage of being able to leisurely line up a shot and catch the enemy off guard. If the goal of SoC's aiming system was accuracy of any kind, than it ultimately fell short by making the player more inaccurate than they should be. Still, later weapons make it not as much of an issue, so the game kind of balances out a bit; Clear Sky, on the other hand, blows goats in that regard.

It's bad design when the player can't trust his own control input to be accurately represented in the game.

You move when you press the move keys, you shoot when you press the left mouse button, and you aim when you move the mouse. Your control input is accurately represented in the game. And it's not like the inaccuracy is unpredictable. If you aren't able to hit anyone at a given range, evidence suggests that finding a way to move closer might help. It's supposed to lead you to a different sort of playstyle than other FPSs.

Why is that a design flaw? Inaccurate weapons used to encourage you to advance and flank seems like pretty reasonable design to me.

*Some* inaccuracy is good; ideally, there should be some stat based inaccuracy, but just enough to account for the limitations of human reflexes, and even that should be reduced to virtually nil if the player is in a situation where they have all the time in the world to line up a shot on an unaware enemy (provided that the weapon is in what could be considered its effective range). A system like that still encourages maneuvering (after all, the enemies' bullets still hurt regardless of how accurate you are), but it doesn't result in stupid scenarios wherein I need to be right on top of the enemy in order to have reasonable accuracy in the aforementioned scenario of drawing a bead on an unaware enemy, which then results in me being seen and proceeding to try to occupy the same space as all the bullets in the world.

tl;dr: inaccuracy alone isn't the problem, but the degree of inaccuracy is far more than it should be, for the reasons I gave in the text you quoted: namely (1) the stat induced inaccuracy tries to account for "combat stress", something that is already simulated by human nerves and limited reflexes, thus failing to simulate any kind of remotely feasible actual gunfight not being fought by someone with some sort of nerve damage, and (2) the "combat stress" the game seeks to emulate applies in scenarios where it has no business applying (see the sniper example), again failing to reflect how an actual gunfight would play out by making the player's guns overly inaccurate.

Sure, it's not a perfect system. SoC is far FAR from a perfect game. But it works fine within the context of the game, provided you actually try to adapt and adjust to it. Situations where you have to attack an unaware enemy and aren't able to move into an effective range are few and far between. Hell, situations where you have the opportunity for a surprise attack are also few and far between. Put simply, yes... the situation you describe isn't realistic. But far more often, you're in a situation where the inaccuracy is realistic. And after all, the reverse is true of most supposedly "realistic" FPSs (Insurgency, ARMA, Operation Flashpoint, Red Orchestra 2, etc), in that they are unrealistically accurate during combat and only realistically accurate in moments where you really do have time to aim and aren't under any stress.

As I said before, there is no situation where using a mouse to position a crosshair over a target is anywhere close to aiming a real gun. Real guns are heavy, and relatively hard to aim, since you actually have to use your own muscles to support them aind keep them on target, and there are a lot of ergonomics that can throw off your accuracy. The way you pull the trigger, whether you flinch or not before the shot goes off, how it's resting on your shoulder, even how you breathe. It's also relatively difficult to keep the weapon straight. And this is under the calmest, target-range circumstances. A mouse is an extremely precise instrument in contrast that can be kept incredibly steady even under the most "stressful" of circumstances (and this is even pretending that the stress of a computer game is anywhere close to the stress of a real life firefight).

And even if you discount all this, that still doesn't mean that STALKER's inaccuracy is bad design, because a lack of realism doesn't equate bad design. In this case, it just means that there are certain strategies that don't work. Namely, trying to be stealthy and pick off enemies from a distance.

Stretched for time, so this is all I can address at this point. Lack of realism is not always bad design, I agree; I'm not going to argue that Doom sucks because of the player storing weapons in his transcendental pockets. However, where (1) realism was the goal of the system and (2) the lack of realism screws over the player, a lack of realism is absolutely bad design. Forcing a player to get closer is one thing, but if at a range of 50 paces I have a headshot aligned on an unaware enemy I can't reliably hit the enemy, then something is wrong. That said, later weapons do negate that kind of nonsense.

If you lock an MP5 in a vise, it doesn't shoot bullets in a cone with a meter-wide spread at twenty meters. The ones in the game do, however.

That's because the weapon isn't in a vice, it's in the stalker's imperfect hands. There's really two options when it comes to simulating the imperfections of a person's aiming in a video game. You can do the weapon-sway thing where the crosshairs are moving around all the time, or you can have the crosshairs change size to reflect the current accuracy. I'm not aware of any other methods in use or how well they might work.

That said, I like stalker's take on it. I think it was a good design decision. With Clear Sky, I put in the optional ballistics mod. When crouched with the pistol, the accuracy is dead on. You can headshot entire platoons of guys from ridiculous distances as long as you're crouched behind some cover. It makes the game far too easy, even on Master difficulty. Also with this mod, shotguns become far, far more deadly and amazingly overpowered. You can blast away at guys from long distances and you don't even need to be that accurate because the small spread will still get them. Before if you tried that, the spread was too great and virtually none of the buck would connect.

My only complaint is that an enemy's aim does not seem to be affected by his actions. I've seen many enemies strafe out from behind cover and nail me with dead-eye accuracy over and over, and then when they peek out crouching they'll frequently miss.

Yeah, as far as I've ever seen, the enemy doesn't have the same accuracy modifiers as you do. That's a legitimate complaint (although it's perhaps necessary for balancing reasons).

When the enemy is capable of firing through walls in the dark with relatively pinpoint accuracy from the hip while strafing while using the same weapon I have to hold perfectly still to get comparable results, I think balance has taken a few too many blows to the head. SoC does even out the playing field later on, at least, but Clear Sky... all of my hate.

You're forgetting about the hit probability modifiers, which pretty much even everything out as far as I'm concerned. Hell, even with them turned off, I still consider the balance to be pretty even. Have you actually played SoC lately, or are you relying on memories?

Replayed it right before moving on to CS.

If you are using crappy weapons at the start with low accuracy, just get closer while running from cover to cover. And USE the cover! You've got lean keys. Although the best cover is the kind you can crouch behind with only your head peeping out. Make sure the cover is stone/tmetal or a tree or else anything that's a rifle will punch right through it.

Also, basic shoot out 101: Most of the stalkers you go up against have poor trigger discipline, often unloading their entire clips in your general direction the second they see you. The very moment they run out of bullets and start reloading, jump out and shoot them!