Because the weapons are different in each slot. I prefer the kinetic pulse, Nightshade. Lots of people like the Void Nergal. They're similar, but different when it comes to stability, range, and perks. That's for PvP. For PvE, it matters because for enemies without shields...use kinetic! Don't waste your "special" elemental primary ammo on enemies with no shields. Those elemental primary weapons work wonders on shielded enemies! It makes for more variation in your choices, instead of just having 1 primary that does all.