Let me explain.
I know we have the FO skills; small guns, big guns, energy weapons, ect. But, if you were to find a M16 in the wastes, you would have no idea how to use it if the only firearm you were ever exposed to was a pipegun.
So to use that M16, you would either have another player who already 'leveled up' thier skill with the M16 show you the basics, learn it from an NPC, or take some time and figure it out yourself (if your small guns and intel are high enough).
Of course, at this point you would only know the basics; just enough to fend off some geckos. But, as you fight the geckos you learn to handle the rifle better (the cap, and the speed of 'leveling' could be determined by your small guns skill). Maybe you didn't feel safe going straight to the wastes with a firearm you aren't familar with, so instead you spent some time shooting some old cans until you felt confident (max at 50% of the overall cap...?) enough with the M16.
Now, over time, you could become quite proficient with the M16, but you're pretty happy when you find an AK47 in a bandit lair because you know the AK47 won't malfunction nearly as much in the harsh conditions of the wastes as the M16. Because you're familar with another weapon which is fairly similar, you might be able to quickly adapt what you know about the M16 from the AK47; maybe you 'level' the weapon faster, or perhaps you start with a 20% bonus to the 'experience' for the AK47. Maybe both.
Other then the obvious level of immersion this would bring to FOOL, this would also provide a system that rewards players who wish to specialize, lets say become an eagle eyes sniper, without overly penalizing those that want to be a more diverse character, perhaps a crazy chemist who can sweet talk his way out of a grave, likes to get high on the jet he makes to watch gecko heads splatter through the scope on his rifle, which he finds hilarious.
Now in PvP, although the sniper is a much better shot than the chemist, there aren't too many situations which the ability of the sniper to clip the wings off a fly at 300 meters will provide any advantage when compared to the chemists ability to hit a cantelope (just enough for a headshot) at the same distance.
You would really see a difference in PvE, however, especially considering that you're really best off shooting a deathclaw in the eye. But thats when the chemist brings some of his jet addicted buddies and pays them some jet if they live through the ordeal.
Although... in this situation you could combine the two aspects (PvP and PvE). Perhaps the deathclaws are in an old church with a bell tower that makes the perfect sniper nest. The sniper could target a few key deathclaws so he can sneak through and reach the tower, and the deathclaws down below (once respawned) could unwittingly act as his first line of defense from anyone who wants to flank him.
With the chemist, his jet freak buddies could turn the church into a temporary base, and act as his first line. Did i mention i dont see any reason why the jet freaks couldn't be other players, or NPCs?