From the various crafting menu screens we see in the Fallout 4 E3 videos we can learn some fairly interesting stuff about how the game is going to treat damage types and resistances in Fo4.
-First off, armor, or at least power armor, has three kinds of resistances on it. The first is displayed as a shield, the second one a lightning bolt, and the third is a radiation symbol.
-Secondly, during the weapon mod menu sections, we can see that normal guns deal a damage type displayed as a crosshair, laser weapons have the same lightning bolt symbol as PA does, and plasma weapons have BOTH.
-Thirdly, several weapons/weapon mods indicate that frost damage, in the form of cryo weaponry, and electric and fire damage, in the form of weapon mods, will be present in the game.
From this, we can gather that Fo4 is going back to a more Fo1/2 style of damage resistances, with guns dealing physical damage, energy weapons dealing energy damage, and plasma dealing both. As well as there being various fire/frost/shock mods to further influence damage instead of those being stuck on only one or two items in the game like in Fo3/NV.
I suspect that, since plasma weaponry has both physical and electric damage, its going to do the highest total damage, but it is going to be split between the two, offering lower damage on each type then a normal gun or laser weapon does, but allowing them to work on more targets without having to carry both a normal gun and a laser weapon on you at the same time.
Seems like a nice way to balance all three out.