What your saying is true however I found when modding the weapons for the original that it severely broke the game. The dumbness of the AI made it ridiculously easy to slaughter them with the increased damage weapons.
Thats why you also have to mod the AI, its easy enough to do, it just takes some time and alot of playtesting to get it right, but you can make them more deadly than Aimbotting-wallhacking CS haxorz or dumber than dirt according to your wishes.
But you can't really expect the vanilla AI to perform well with modded weapons, they where playtested and balanced for the vanilla weapons, so if you change one, you must also change the other or something gets broken.
You can do alot of fun things with the AI though, for instance they have both a "relaxed" and "combat" mode, so you can enable stealth for instance by making them pretty dumb in the relaxed mode, so you can sneak up on them, but once they see you or hear gunfire, they will go into combat mode, and you can have them play totally different there, and make them extremely deadly when alerted to danger, or not, you can also make them dangerous in different ways, like making them super alert, but not very accurate so they will spam lots of gunfire at you, or make them less alert, but very accurate, so you have to use some more stealth and choose your engagements wisely, you can also make them tougher or weaker to different things by messing around with immunity values, once you wrap your head around all the options that are actually there, there's lots of things that can be done to tweak them to your liking, hell, just tell me what you'd like to change, and i'll point you in the right direction, tell you what code to tweak
But i hear that Clear Skies is doing things differently with its code, time will tell what that means, but hopefully it means coding some things becomes more straight forward, and more flexible, Stalker can be a bit conveluted in its code, and you have to make tradeoff's to get some things to work, and mod alot of different files, lets hope this new code will be more freindly
But this might also mean my prediction of mods withing a week may not hold, if the code turns out to be very different, we'll all have to learn it all over again, and that does take some time, we'll just have to wait and see, but regardless, there's no reason to worry about the combat, i seriously doubt they would shoot themselves in the foot by making it less modable, if anything it will be more modable and have more values to tweak, and we can do even more with this code.