I'm wondering if perhaps it would be a good idea for there to be more situations where a primary weapon could be rendered useless or temporarily unavailable, as at present a pistol is really only good for if a soldier's main weapon is a rocket launcher or something else heavy and the soldier enters a small room or simply runs out of ammo.
Some ideas:
Being hit by an alien plasma shot or blast could cause a soldier to (sometimes, depending on where he/she is hit) drop what they are holding.
Some aliens might be resistant to some types of weapons that can only be made into a pistol or larger rifle. If this sounds confusing, I'll put it this way: A special type of ray gun is needed to hurt or kill an alien, but through R&D humans can only build a weapon that can produce this type of ray in the form of a large, bulky rifle, because it is too difficult to make it into a smaller pistol. By the same token, perhaps a weapon can only be a pistol because it can't be manufactured successfully into a larger device.
Weapons can also misfire, jam, and get damaged by things even as simple as getting wet (water).
Some types of high-penetrating or explosive weapons might not be allowed on some missions because of how dangerous they are to the environment - For example if aliens attempt to attack a nuclear power plant or explosives factory, only certain weapons could be used to avoid a catastrophe. (These might be good ideas for new missions, BTW.)
I'm not a gun expert, but wouldn't some weapons not work in space (in future missions, or if aliens attacked a space station or orbital installation)?