You are absolutely correct, having an element on a primary weapon does not make it significantly better than any other primary weapon without one. Weapons such as Abyss Defiant, Word of Crota and any Y1 Adept Trials Primary (very good, but not suited for PvE whatsoever) are testaments to this. The only thing that comes to mind is balancing for Swords in PvP, as a Primary Weapon with the correct element makes the block pretty much worthless, but Swords are rarely seen and it's not as if you won't get mowed down by something else just because you're using a Machine Gun or a Rocket Launcher.