By the time you've finished the campaign and all the other achievements, you'll probably only have mastered a few of your favourite weapons. There is a fairly straightforward way to boost this though: The game does not care whether the enemies for challenges are conscious or not.
So knock enemies unconscious either using melee or non-lethal rounds, stack them in a big pile, make a save, do what you need to do, reload your save, repeat. It's a good idea to let them sound an alarm so that they'll all come to you and you won't have to carry them so far to stack them.
For the rifles you're going to need a spot where you can hit enemies when they're lying on the ground from 100 meters away, I choose the starting area of level 6 "Assault on fort Rouge", since there's an elevated spot with free line of sight to the ground beneath.
When you're done with one weapon, you can run to a work bench to switch your load out and repeat with the next weapon.
NOTE: The pistol masteries are currently bugged and will probably unlock early. I'm not sure anyone knows what unlocks them but most people seem to report it unlocking very early in the game.