tl;dr version:
- Crafters should need recipes in their inventory so that they're not all the same.
- I like consumables.
- Basic crafting should allow crafters to trade bonuses for penalties.
- I like the idea of charges on enchanted items.
In general:
While a "Gather > Refine > Craft" system would be nice I don't think DnDs limited skill system really supports it. In almost every case the skill that would be used to gather the resource is also the skill that would be used to refine it making the distinction between gathering and refining pointless (except perhaps to limit the ability of harvesters to carry large loads?).
More specialised materials would of course require a higher DC check to collect.
Some of the gathered materials could even be useful in their own right e.g. a half dozen healing herbs could be used by an alchemist to produce a more powerful healing potion.
Given the raw materials a crafter would produce an item at a specialised station of some kind; possibly requiring a recipe in their inventory for the given item to represent necessary training or tools that they have acquired which would allow various crafters to differentiate themselves.
Maybe different crafting stations could offer bonuses (e.g. the publicly available stations would be of the lowest quality, guilds would be able to expend vast quantities of space and money to get facilities that provide a bonus? or permit certain more complex recipes to be used?... I have no idea the limitations of the game engine here but I like the idea) to allow groups to be specialised in certain areas.
The crafter would of course have to expend a pile of gold (for materials apart from the specialised ones) and pass a suitable check to make the item (losing some or all of the materials on a failure, actually now that I think about it: I rather like the idea of fairly low DCs but poor rolls requiring more resources than a good one... not sure if that's manageable though).
Consumables:
I would love to see more consumables being produced, or even just available for sale.
The whole gamut of the base alchemy items (tanglefoot bags, acid flasks etc...) plus grease bombs, glue bombs, smoke bombs, poisons (and on a side note I'd love to see poisons made deadly, with Deathward preventing all statistic loss they're kinda pointless), myconid spore bombs, caltrops, oils of resistance, scrying stones, magic ropes (bypasses climbing check), weapon oils, whatever the sick minds of the server can come up with.
This would provide some variety to the basic combat classes and something of a stealth nerf to the caster classes by "open sourcing" some of their weaker spells.
The high-end consumables (e.g. the OAD&D oils of resistance) could also provide something of a gold sink.
Mundane Crafting:
In addition to the expected arms and armour I think it would be good if crafters could produce placeable props, ammunition, healing kits, lockpicks and other mundane equipment.
Personally I have never liked flat "EB" weapons and armour, I've always thought it a bit silly for a wizard to have crafted "The swordiest sword that ever did sword".
If it were possible crafters could "juggle" the stats on the arms and armour they produce, trading bonuses in one area for penalties in another (e.g. your elvish swordsmith could produce a "rapier of extreme pointiness" with a large hit bonus but damage penalty) or special features e.g. bleeding or keen; all of which would increase the DC of the creation.
This would also alleviate the problem of "casters will just make weapons without any EB bonus and use GMW" since the basic bonuses wouldn't be added by enchantment.
Of course special materials would be possible but would be very difficult to obtain and might require another crafter to turn the raw materials of one kind into the base materials of another (e.g. taking a pile of mithral slivers and turning them into a mithral ingot).
Enchanting:
Instead of slots I favour the idea of horribly high DCs for enchanting with later enchantments increasing the DC further... not sure which skill would be used though: spellcraft? This would mean that a given enchanter would be able to safely add a certain number of bonuses to an item and then it would become risky to try any more, it would also mean that you could take your favourite sword and enchant it, and as your career continues and you have access to more funds you can add more abilities to it, or that you may have to "shop around" multiple enchanters to get the final item you want.
I do like the idea of enchantments requiring charges (although I feel exploding the item on a recharge might be a bit much) although some enchantments (e.g. light) should probably just be permanent and in some cases the abilities would need to be instantly activated ("Hold up! I need to find the matches so I can light my flaming sword").
I feel enchanting should also require materials, recipes, and knowledge of specific spells to again differentiate different crafters and to somewhat limit the power of money.
Caveats:
I have no idea of the limitations of the game engine or the limitations of the patience and skills of the scripters and devs.
Common resources (e.g. herbs for potions, iron ore) would have to be just that: Common, possibly even available from shops. If everyone is drawing from the same pool of resources they will be exhausted moments after each reset.
Rare resources will need to have random placements otherwise you'll have dedicated "harvesters" grabbing it all: preventing others from participating and cornering the market on those materials (somewhat defeating the point of a crafting system).