It's a combination of bad aim and people not understanding the weapons don't do similar damage to enemies. Let me use Uncharted 1 as an example (as it's where it is most obvious).
In UC1, the pistol you get at the beginning of the game downs enemies in 4 to 5 shots (to my recollection, I could be off by one more bullet and the 92-FS kills in 4 shots instead) while the AK-47 takes more shots than that to down someone + the longer you hold down R1 the more erratic your aiming becomes which means you have to compensate that with the analogue stick by holding down to keep the reticle steady. If you burst shoot the AK-47 you'll be more likely to down enemies reasonably but if you hold R1 then it's harder to down an enemy reasonably, especially because in UC1 they do a dodge and aren't just standing there waiting to be shot.
Not only that, but people likely aren't going for headshots as if you would it only takes 1 headshot to kill any enemy in the game (except for those with helmets, you have to shoot twice: once to remove the helmet and another time to hit and kill them).
Bullet sponges don't exist in any of the games in their original PS3 incarnations if you know what you're doing. If it's taking you an entire clip to kill someone, you're bad at the game. Simple as that.
