I think one of the easiest ways to make guns scary is to just make it possible for a single crit to put a PC into negative wound points. It wouldn't have to be guaranteed, but just having even the smallest guns do a maximum of 10 or more damage would go a long way towards convincing players to really be sure before they bring out the guns.
This would make sense for a "realistic" campaign quality. On that note, what is the default "realism" for a Spycraft game? Cinematic realism or something more lethal out of the box?
Of course, I am of the opinion that any bullet is just about as deadly as any other bullet, and the benefits that big bullets have over small ones is better penetration and better accuracy over long ranges.
I would agree with that when talking about the same types/categories of firearms or saying that all bullets can be lethal. That being said, the odds of someone surviving a pistol round to the body are much higher* than those of surviving a rifle or shotgun round, especially
with modern medicine. Of course, survival
does not mean getting up and kicking the crap out of the bad guy that just shot you...
And about fearing the NPC guns, don't forget about the Marine who caught nine AK rounds in the chest at point blank range and walked out with a couple of broken ribs.
What about the Highway Patrol officer who caught a single .25 caliber pistol round in the armpit (where I've never seen protection in any
armor) that went between his ribs and clipped his aorta. He bled out in less than a minute, but not before hitting his assailant's center mass with five of the six hollowpoints in his service revolver. His assailant survived with five slugs in his fat belly, his jean jacket preventing the hollowpoints from working as designed.
Weird things happen.
*One of the firearms instructors at the law enforcement academy I attended said that, statistically, people had a 90% chance of surviving pistol wounds. That chance dropped to 10% when dealing with shotguns and rifles. Of course, part of that training was to develop a survival mindset, so he also talked about how movies and television shows have conditioned people to think that they are supposed to fall over and die when shot, regardless of weapon used.