I think perception was 9 or 10 so not that low a penalty, it doesn't really matter though, like I'm saying I debug'd so firearms and handgun (and all skills) were something like 30-40, the piddly -1 or -3 penalty should be outweighed by the extremely high accuracy bonus guns and firearms gives.
You're thinking like a gamer
A "bonus" from skill doesn't negate having low perception and dex, no matter how high it gets. If you're physically incapable of holding the gun steady or percieving the target properly, no amount of skill is going to make up for it. Likewise there's only so much accuracy you can get out of a crappy gun, no matter how good you are at handling it. Basically it's about removing obstacles to accuracy rather than stacking bonuses, which is how it works in reality.
Optimal accuracy requires:
Firearms 9
Specific skill (pisol, rifle, etc) 8
Dex 12
Per 12
No arm or eye encumbrance.
At that point the only sources of inaccuracy are the gun, ammo, and recoil.
With those stats and a really accurate gun and ammo, (one of the hunting rifles for example), you should be headshotting things at the edge of visibility. I'm not going to claim it's optimal, at best it's "reasonable".
Those stats and skills have other effects besides increasing accuracy, such as accelerating reload times, reducing recoil effects, and recovering from recoil more rapidly. Also for the stats in particular, having higher levels provides a buffer for the many, many things that can reduce them temporarally.
I'm working on a refinement to the system that will increase intrinsic accuracy of guns and ammo, and add a dynamic aiming system, so guns will be accurate as hell, but only when you take the time to aim. Right now I'm snowed under with merging and putting out fires, so that's on hold