I suspect the real reason crafting systems aren't in D&D but are in MMOs and CRPGs is a simple one: MMOs and CRPGs can afford to make pre-defined effect combinations because the players don't generate the electronic content. (Second Life is somewhat interesting, as it works somewhat differently, but it's not nearly as successful as WoW because it generally relies on players to generate their own content to have any fun. And doing 3D skinning, modeling, and coding is a set of tasks many don't want to do.) No matter how you look at it, crafting systems basically work on a single principle: combining item/ability X and item/ability Y creates item or ability Z. In recipe-based games, the "recipe" is effectively a part of the combination that often becomes a permanent part of your "inventory" once obtained. In base + modifier systems, it's simply a matter of finding the combination of sub-effects and modifiers that is closest the desired result. The gadget system in d20 Modern is effectively somewhat like this, as gadgeting adds new, pre-defined qualities to a base item for a certain cost.
On the other hand, when you have unlimited effects creation, you get a case where it's a total ***** to adjudicate what the appropriate "costs" are. And if you make things profitable... well, it creates positive feedback. And there's no game balance in positive feedback to character power, unless it is paired with a source of negative feedback somewhere to create a sigmoid curve in terms of power from a certain source. (I suspect that the best games balance things in this manner; it would certainly help game balance issues if you can always expect character power to be within some value X of the "ideal.)