With the firing AP cost of shotguns so high and without the option of burst fire, I figure you can increase the damage shotguns do by quite a bit. For example, even at 25-60 with a 2/1 damage modifier from 00 buckshot, it only takes a 5-round burst of JHPs from a .45 ACP SMG to do even more damage, and that burst costs less AP.
That might be overdoing it, but even with full length shotguns doing something like 26-36 (with x2 from 00 buckshot), they could be given a significantly more poor DR modifier, to the tune of +35% - +45%, and they'll still do some damage against, say, Metal Armor (17.1 with +40% to be exact, vs. 18 as it is). Beyond Combat Armor, I'm quite comfortable with shotguns becoming obsolete.
The ranges aren't a big issue as long as they're more than ~20, since long range combat is pretty limited. The 40 of a Kar98k just looks odd next to the 35 of a PPS-43.
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Do you know what the mechanism for determining bonuses from special abilities like Accurate, Long Range, Scope Range, etc. are? Or, for that matter, how the actual range, the Range attribute of the weapon and other factors affect the hit probability of shots? That would help immensely in what stats to give which weapons. I was thinking of doing it the other way around -- giving manual action long arms (and those weapons renowned for their accuracy) the Accurate ability and all other rifle-caliber weapons with longer effective ranges the Long Range ability, MGs and battle rifles included -- but your way may well work better.
The longer effective range of MGs I simply handled by giving their burst fire a longer range -- e.g. I have the burst fire of an M14 a range of 30, that of an M14E2 a range of 40, a BAR 50 and an M60 60. Since I don't know how the Range attribute factors into the hit probability calculation, I have no idea if that works or not.
Speaking of hit probabilities, do you know whether the AC % modifier of ammunition is limited to reducing the AC to-hit modifier from armor to zero or will it, as I expect it does based on playing around with it, reduce AC below zero, effectively being a straight to-hit bonus? If it's the latter, giving the large caliber rifles a -35 AC % modifier might make hitting with these guns at longer ranges a tad too easy -- by which I mean 99% always except at extreme range in pitch black.
Also, a -35% DR modifier effectively makes the DR from any armor other than Advanced Power Armor useless. After all, these are only lead-core FMJs, all of which are handily defeated by ~3mm RHA. I suppose whether you consider that a problem depends on how useful you want body armor to be.
One idea for making ammo conservation a serious issue: reduce the ammo box sizes across the board. For example, dropping the size of a 12 gauge 00 shell box from 50 to 7 cartridges, even if you also cut the price by 6/7ths, would suddenly make you think a lot harder about shotgun ammo expenditure -- something that's not really a problem when you can buy about a thousand 12ga rounds on one visit to NCR.