On nerfing
There are only a few things things here mentioned that I can honestly say need nerfing. Please don't.

I saw some npc merchants are no longer buying scrolls. This change made me sad.
On enchanting:
Please, don't make this harder than it already is. I've blown up tons of crap and had one, ONE successful enchantment this month alone. The menu could use a clean up (ex: container enchantment when cointainers aren't avaliable on arelith, for example). Maybe a boost with some things to encourage some vareity. (1d4 massive crits is not very useful)
Yes, you can get nice stuff. Stuff that spanks the pants of craftables. This is for two reasons.
1. There are very few end-game craftables. Or even acceptable mid-level craftables
2. Enchanting has far more flexibity
That said, as someone thats done tons of enchanting and played an epic enchanter? It takes an absolute shitload of gold and time. It might reward some rich people, but it absolutely and utterly punishes the hell out of the enchanter with the xp loss.
On crafting:
This definately needs a boost. Some of this stuff has been around for over a decade, and was NEVER useful or widely crafted. Like hunter said, there are only a handful of end-game things avaliable, and the in-between's aren't that good. Some stuff has been flat out ignored. Examples?

The repeating crossbow has a whole +1 ab and a limited use of manticore spikes. We have gonnes now, so that only feasible use this thing might have is completely gone (lower levels making mass-volley shots at a lone target in groups). Yes, the charges can be reloaded with another craftable, but if one serves no purpose and is never used...well. The other has no point either.
:Arrow: There are no craftable bracers. There are no craftable rings or belts that have any additional properties.
:Arrow: A lot of stuff is from the gigaschatten era, and, coincidentally, most of the end-game-ish gear is best suited for bard/sorcs. The only +2 stat items that are craftable are all CHA based. Most wearable items have perform/persuade bonuses, which are only useful/attainable by bards.
Don't believe this favoritism was intentional? Look at the fur cloak. Its price was artifically lowered by something like 20k. And its something that, with a bit of luck with enchanting, can easily compete with the best of from-scratch basin work (+3 fort saves? yes please)

A bunch of changes were made to quarterstaves to make them move "combat friendly" (I use that loosely; making them double weapons was a terrible thing) but there are only a very small handful of craftable staves that cater to meleers.

Portal lenses require gems that take +3 RL hours to obtain, and have been made incredibly fricking difficult for a party that isn't a balanced-epic sort to find. Or, dragonkin farming.

Some craftables that might be useful for basining are utter crap due to artifical price increases. The cloaks of +5 skill are all artifically set to 10k, making any and all enchanting a 5% chance.
So on. I won't nitpick every last thing, but the point is crafting in general could use a good re-examining.
On resources
Some of these could use some tweaking as well, but not nearly as much as crafting.

For the love of god, make plant-resources respawn like everything else again. I don't think i've been shy about my hate for this, but its encouraged players to spam plant-placables EVERYWHERE because its completely normal to only get one use-per-reset out of plants. Its also made things like berries harder to find than masterly damask weapons after the first two hours the server has been up.
Druids never made a huge % of the playerbase, and the ones that are on probably have better things to do than tend every last plant on the island over and over as settlements/crafting hoarders nab that crap immediately after you tend to the plant (literally, following right behind you)
Reverting the system would help with clearing the mass of plant-placables, which would improve server performance. Sure, it'll happen again eventually, but it won't be as fast/as frequent without the incentive of "as much as possible because of one-use-per-reset". Seriously; look around the east arelith forest and count how many crafted-plants actually have a name or description.

Some mineral/gemstone drop rates are wierd. Smacking a deposit for 50+ damage a hit consecutively should drop SOMETHING, especially if it involved an epic, hour long trek though some of the most dangerous areas on the island.
When a good portion of the high-end crafting recipes depend on said resources, it shouldn't be a surprise when suddenly said craftables are stupidly hard to reliably come by.