The best way to balance it would be to take it as three types of weapons.
1- Stuff that requires ammo, bullets, rockets, etc etc.
2- Energy weapons
3- Remaning weapons.
type 1- Assign a base damage ammount to all ammo of this type. From there, each weapon that uses the ammo can alter the damage by up to five points with at most a few exceptions (sawed off shotgun would offer greater damage, but have shitty range for example)
Type 2- Make energy weapons (flamers would count as such for this case) fit in the balance better. They dont do that much more damage, but can bypass armor better.
Type 3- Grenades, mele weapons anything else, gets in here and gets balanced based on how such a device would compare to the real world guns (a known quantity) in damage. Grenades would get a substantil boost (plasma even more so) while mele weapons are only useful against light or no armor, aside from knockdown values (cause lets face it, Im wearing power armor, and you hit me with a sledge hammer, you wont do much more than knock me down and slightly rattle me with the fall, where if Im wearing a leather jacket its still gona fucking hurt)
It would also require a total re-balancing of armors too, or even of damage resistences prehaps. If possible, add new resistence types. If not, then combine laser/plasma into energy resistence, and use the now empty slot for something else, impact resistence prehaps (AKA, how well it defends from something hiting you hard, such as a sledge hammer for example).
Past that, play around with amo types. Holo points= great against unarmored targets, but if the target is hardend (metal armor on up) they do a lot less cause they deform too easily. jacketed holo points can penetrate armor much easier, but still dont do that well against harder armor. fulll metal jacketed rounds would have lower base damage, but be much more effective against armor. For larger type rounds, allow for things like armor peircing rounds and other types. For shotgun's, take one of the few things that FOTactics did right and add in multiple types of shells. Slugs have high knockdown and armor peirce. Standard shot is less effective against armor like hollow points, but vert effective against unarmored/lightly targets, flechettes would be VERY effective against soft targets. Also, if possible re-adjust how shotguns work so as to simulate firing a spread of shot. If the shell holds X ammount of balls, then increase the ammo capacity of the weapon by that ammount, and make the defualt single shot a burst so that it spreads out more and can hit more than one target. Then just increase the ammo expendeture for the real burst effect in the case of automatic shotguns.
Also, it'd be cool (and add to the RP options) if someone made more ammo types for the needler pistol.
A poison round, does dammage over time.
Sedative round, can KO a target (and add options allowing for capture, robbery, or even slavery) and whatever drugs/chems you can think of.
Ditto for regular guns. Rubber bullets could be used by some towns police forces in cases of civil unrest (id doable, code it so using that type of ammo doesnt count as a lethal attack, but rather makes people even more likley to flee if its a more cowardley characther, plus would add options such as dispersing a bar fight, spray it down with rubber bulets, they get the picture, stop.)
The KEY tho is to make most regular pistols equal, based on type of round, and the same for rifles. Then suddenly a 10mm pistol is almost as useful as a 44magnum instead of a joke in comparison.
Shotguns, if it is possible to use the method I mentioned above to make them simulate firing shot, should have their range extended a bit, but should be re-designed to spread out a by a VERY great deal so that at max range, you could potentely hit people over a 10ish hex area. (which means you have to consider how to use them in populated areas).
heavy weapons, The rocket launcher should be increased by a large ammount in damage. Lets face it, unless you're in power armor or lvl99, its going to kill you with a direct hit. The armor peircing one should only effect a 1-2 hex radius around the impact point, the explosive round should affect the surrounding 3-5 hexes.
heavy automatic weapons shouldnt be nerfec like they are, if I remember rite ( dont feel like looking it up) their base damage per round hit is lower than other small guns that use the same round, that should be changed. It will make the miniguns much more lethal (all automatics really) and require some use of tactics, or bugging out.
Gauss weapons should be handled differntly, not sure exactly how but they should be among the most powerful single shot pistol/rifle's, and bypass a good % of armor as well. They should also have a high knockdown chance too.
Grenades should do 100+ points of damage, and affect a decent area, 4-6 hexes
Plasma grenades 20-30 points more than that, and affect a similar area.
in essence, if the gun types use the same ammo the damage output should be very close if not identical, this makes some guns stronger and some weaker, but actualy balanes them for more fun casue you get to pick a weapon more for roleplay reasons w/o being penalized .