Here's my idea:
Make it so we can make some of the base craft components so that characters who don't want to be or shouldn't be involved with the NPCs. Calibans, outlaws. Really, it has application for characters who have taken oaths not to have money and other such goods as well. Essentially - all the bottles, alchemical containers, smiths tools, leather working tools and everything else can be made by one of the other crafts so as to make a player-run economy more viable - and easier for the not-so societal acceptable to participate. It still works on punishing wicked Caliban, it'd still be hard and would make it more tedious.
(Pros): Players can do stuff, even when the merchants are dead/broken. (Or if it seems viable, maybe even remove them at some point?
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(Cons): Work for the developers (not sarcasm or anything, I'd understand it'd take a bit of work).
Another suggestion: With all this in mind - could we have it so herbalists could actually make healing kits? Have it be 1 benifical herb, 1 cloth/leather/fabric, 1 metal tool, etc etc etc. So that we can actually make these ourselves? The items don't cost much as is, so if they were made to be based mostly on the players that'd be cool too.
I mean given time and the removal of some of the NPCs (or their infinite inventories) it could actually make your weapons, resources and other such crafts actually.. useful and worth it, despite not being as impressive as the higher end crafts like herbalism, alchemy, and enchantment. It would make it so players had to rely on themselves and other players to do these things. I don't know, I think it could be really cool.
What do you think? I mean it doesn't be as hardcore as I'd like to see it, but it'd be amazing just to have that ability. I was playing a character the other day that didn't believe in society or money so him buying these things was out of the question.