Some problems I spot:
I said it was probably terrible.

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1. Your chance of getting a really good hit has nothing to do with your skill and everything to do with whether the target glitches on their body+armor roll (which is very unlikely if they're wearing decent armor).
Agreed, though this was semi-intended. In order to really, really hurt someone, you have to hit and they have to botch.
Called shot rules could fix this (take dice pool penalty to start damage at higher tier?).
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2. If you allow smartguns to reduce accuracy by 2, you pretty much have every hit doubling accuracy (or more), since this will make almost all of your listed accuracies 0 or 1. There is no way to handle an accuracy of 0. Probably want to set a minimum accuracy of 1.
Accuracy 1 would be the bottom, yeah. Some thought would have to be put into the weapons, or maybe Smartguns would just have to be -1 Acc. Accuracy higher than 4 would be reserved for really, really inaccurate things.
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3. A low accuracy is good, while high everything else is good (that can be confusing). So a high accuracy weapon would have a low accuracy number. Consider renaming it to make it something more intuitive.
This is true. I was reusing terms instead of thinking up new ones.
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4. Penalties stack up quickly under this system, so you'll get the death spiral. Not something I actually mind, unless it leads to the irritating thing where no one can hit anything and the fight drags on. Consider whether you think the death spiral is a feature or a bug.
Feature-ish. I think that SR4/5 damage doesn't cause enough of a penalty.
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5. Fights will take longer under this system, since there is more to compare and it's very likely that any character with a body of 4 or more is going to take at about 3 shots to drop unless you're using something bigger than an assault rifle and it's nearly impossible to drop someone with even an assault cannon in 1 shot, unless they have a low body score. Again, not sure if you consider this a bug or a feature.
It's about the same amount of comparison. There can be guidelines that suggest dropping mook NPCs once their damage passes their Body/Willpower score, rather than rolling for them.
This can bring Called Shots back around -- defenseless guy shot in face = dead guy.
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6. This is still mechanically very similar to damage boxes or the SR1 system, but with less granularity.
Yes, it works out that way. Instead of damage tracks and fiddling over taking 4 points or 5 points or 8 points, it's just a simple scribbled "L" or "M" or however.
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7. Your ROF statistic means that there are going to be even more attack rolls to make on each turn and I'm pretty sure from just eyeballing the math that a light pistol becomes by far the best weapon in the game for everything but trolls. (three attacks a turn, with a smartlink accuracy of 0 (assume 1), so it's impossible to get a glancing blow and with a decent skill you're probably looking at 3P or 4P everytime)
Even at Acc 1 it doesn't scale that fast. 1-2 net hits = Power, 3-4 = Power x1.5, 5-6 = Power x2. And generally no AP.
Acc 2 1-4 = Power, 5-6 = Power x1.5, and so on
If you're getting 5-6 net hits, you're doing pretty well for yourself and deserve to put out a hurting. Light pistols start to lose effectiveness against heavier armor, while heavier pistols stay for awhile past that.
8. Your chances for severe trauma and incapacitation don't make sense, since the Body is automatically eliminated from those rolls (since you subtract the wound modifiers from the Body+Will and you don't roll until you're at a negative equal to the Body score). I get the staying conscious, but a strong willed character is less likely to have a specific trauma? Unless you meant the accumulated modifiers beyond the body score apply on this test, in which case a high body character will likely stay conscious for many shots beyond 3 or 4.
I know. This part's a bit of a mess.
9. I'm not seeing the narrative control in this system? Did I miss it?
I wasn't shooting for additional narrative control in this batch. If you've missed anything, it's that I like to make systems.
10. Added Complexity
Current System:
Roll opposed, compare rolls, add net to weapon damage, subtract AP from target armor, roll soak, subtract soak from damage, subtract damage from boxes= 7 operations with comparisons, addition and subtraction(yeah, there can be more with modifiers and bursts, but that's true both ways)
Roll opposed, compare rolls, compare net hits to weapon accuracy, determine power, subtract AP from target armor, roll soak, compare to power, apply damage = 8 operations with multiplication, comparison, addition, and subtraction (multiplication, especially by 1.5, takes longer for people to do than the other operations)
It seems like it needs more tuning and some play testing, but I don't see this actually making the fights any less- "I shoot, I hit, I do X damage" and it might push it in the other direction.
This has had no tuning and no playtesting.
A lot of the complexity can be handled in advance, especially the multiplication. A gun with 2 base Power does 1, 2, 3, 4 for its glance/hit/better/betterer categories, which can all be written down with the weapon and referenced quickly. A gun with 3 power does 2, 3, 5, 6 (assuming round up). A gun with 4 power does 2, 4, 6, 8. And so on. With net hit ranges attached.
The burst mechanic I think is simpler mechanically: add one to everything, subtract one from defense pool. Double it for a long full auto burst.
It's slightly different in tone, since it's shifted away from doing 2, 3, 4, 5, 6, 7 8, 12 points of damage and toward doing "a graze, a hit, a good hit, a really good hit."
Narratively it could use some work.
(I ran out of allowed quoted blocks, so italicized means quoted.)