Crafting stuff in games is really hindered by the fact that it is so discrete, compared to the continuous game world. If there was a way to make items work based on something continuous, that would change everything.
EDIT: Good example of that is making sword in games. Usually you only need a smelter, fuel, iron ore and some time. In real life, you need to control temperature (too low and the material cannot be easily deformed by hammer strikes, too high and it goes full liquid) by controlling the amount of burning fuel and creating an air current, then you use your hammer to deform the material the way you wants, each hammer strike also making the material at the impact point somewhat different by creating dislocation and texture, then you cool it off in the cold water so fast that the high-temperature defects cannot escape from material in time, which makes it less deformable...
See how actually involved that process is? I wish the games actually had something like that...
There are multiple ways of doing this in a skill based and a less-discrete fashion. Two examples:
1) Physics engines. Actually model at some degree of abstraction an item as a physical model. And then require some number of variables controlled during construction. If your quenching was incorrect, don't stop you from doing it, just give you a more brittle or soft sword, that actually is more likely to snap or bend in combat. Etc.
A sufficiently advanced physics engine could even let you invent things the programmers never envisioned based on your actual craftiness. Like "grab an old power cord and rip a piece off of a garbage can and bend it and lash it to a broom, to make a thin steel shovel." The engine provides actual environmental materials + an interface for tying and bending and otherwise manipulating things. Then when you actually go to dig with the thing, the engine calculates its failure from actual physical stresses.
2) Gonna throw out puzzle pirates again as an example. It is a rigid system with rules, but still rewards skill and actual craft of a sort. In that game, players "craft" all the cannonballs and rum and ships and swords and clothing and everything themselves. Every single industry has its own puzzle. The puzzle is an abstracted logic type game of the flavor of the industry (distilling, for example, is a bubble swapping game where you work out impurities and try to blend in spices and things into cleared rows). The better you do, the better quality grades the finished goods have OR the longer it takes you (more puzzling sessions), depending on the industry (some goods don't have qualities, so it does time). So there is actual player skill involved in every industry, and hundreds or thousands of discrete levels of points that are meaningful in terms of quality or speed of production that make you more or less competitive as a businessperson.