Mostly because using heavy plasmas for the 347th time you complete the campaign can get a little boring.
Exactly. There should be a strategic/tactical motivation for doing that.
Perhaps a mod that makes plasmas super expensive to produce, and as for recovered ones they have a chance to malfunction and die after a mission in which they were shot at least once
- plasma pistol 50% chance
- plasma riffle 80% chance
- heavy plasma 90% chance
also, plasmas could be made less accurate, especially heavy (though give a bit higher aiming skill to aliens), and then gauss would be the super accurate weapons