The Pulse Rifle is now the game's Scrappy Weapon... because it's a gun built to kill living human enemies, not undead monsters that only stay down when they're dismembered. Against Necromorphs, it's outclassed by all the repurposed industrial tools lying around the USG Ishimura.
Related to the above, why was the crew of the USM Valor so easily overwhelmed by Necromorphs? Because they all came armed with Pulse Rifles, which are of limited use at killing Necromorphs!
Not to mention that it's unlikely their Pulse Rifles were fully upgraded ones like the one Isaac can put together. They were probably unaltered guns at base specs so as to stay in budget, so while Isaac's could probably handle Necromorphs fine with investment on his part, the Valor troops would have been using the equivalent of paintball guns against the Necromorphs.
