I'm not sure how much of the current skill system is permanent. Here's my thoughts:
Obliterate leveled skills, and split the uses of those skills into stats and regular skills. Limit Q by stats, perhaps combination of stats- for instance, some wood crafts might use dexterity and perception to determine Q, while perhaps a sword would take strength and intelligence. Similarly, using specific weapons and maneuvers would tie into specific attributes. This is because the FEP system is unique and has a lot of potential; making it the drive the game would be a bold departure from normal kill-centric XP-based design.
Then, split up the various skills so that there are several sub-skills. Rather than metalworking unlocking virtually everything you can make with metal, have Forging, Tinkering, Blacksmithing, Coppering, Tooling, Casting... so that you can gradually develop a number of skills while remaining specialized. As it is now, It costs far less to learn how to craft metal from scratch than it does to learn how to very slightly improve your grain harvest.
Make it so that specialization is attractive by having self-reinforcing cycles- for instance, having most fishing gear gain from being used with high intelligence; but encourage diversity and trading by having at least one other requirement such as perception, constitution, agility... which is best collected from other skills. Having only one of these either makes trading unrewarding because you can just keep cycling your own skills up endlessly, or making specialization impossible since you never have the resources you need to increase in skill enough to trade for the resources you need.
Consider granting FEP from non-food activities; anything from daily rituals involving items to perhaps quest rewards. This would help make it possible to make more self-reinforcing cycles; metal trinkets might be needed for a Morning Meditation of Strength ritual, for instance.
Now, currently leveled skills do have one use: they act as one endless LP sink. Unless LP reward was decreased or some other sink introduced, claims would tend to grow a bit more... but I'm sure that an elegant solution could appear. Perhaps LP itself could be removed as well somehow?