I dont know how exactly the crafting system will look like, proceed to read this with that knowledge as I might be suggesting something that might be already in the works.
By advancing I mean making the crafting part of the game just another part of a bigger system. Skills such as crafting improve over repetition of tasks and achievements in the game, this means that crafting will also be restricted. Basic stuff using common materials should be at a beginner stage of the skill level and as the player advances his skill he unlocks certain crafting abilities, like making guns, or repairing items. Not to forget base-building, and in this case, people with lower crafting skills can only use materials that are common and easy to gather, and build stuff that is easy and basic to do. Advanced players will be able to use their skill to build complex building parts, doors, windows, barricades and traps in that order.
Crafting would be one of the skill sheets availible for the player, so skills such as cooking, gun-related and other skills would follow a similar pattern.
Let me know what you think/