Many people have been calling for an end to crafting, or to focus on this or that vs. new additions to the game. A big issue is that there ARE a lot of different systems that have been added to the game over the years, from alchemical crafting to Shroud, Reavers Refuge, and so on. What I propose is not to eliminate all aspects of these systems, but to unify them into a single coherent system that still requires going to the various areas.
For the Shroud, there are some unique elements there. First, the idea that you are creating the base green steel item from scratch could be changed a bit so you make a new shard from those ingredients, and THEN combine them with a base "craftable" item to make it a green steel blank. This is required since the power shards you can make in the Shroud(as well as Shavarath) will ONLY bind properly to a green steel blank. In a way, this adds a step to the process, but it also helps unify the idea that crafting is crafting. You still can only make a green steel shard out in Meridia(same ingredients, just you make a shard from it). You might also need a special crafting station, or not, to combine the green steel shard with a prepared base item. Due to the nature of the green steel shard, it automatically transforms the base item into a green steel base, no densewood greensteel items or anything like that, but it DOES give us the full set of items, heavy as well as light crossbows, and the green steel itself just imbues that set of attributes onto the base item. Upgrading is the same thing to add each tier of effects.
The side effect of adding it to the same system as Cannith is that you can "deconstruct" it now, with the potential for returned ingredients.
SoS/Reavers Refuge could also benefit from this approach, where you are getting imbued power shards from SoS that you are adding to the base item. The base items could get an upgrade in the same way, where you take a base item, upgrade it to a Reavers Refuge item(remember RR items are better than the usual item of their type) as a part of the reward(no more them giving you the item you request, they give you a shard that upgrades an existing item), and then we go on from there.
The real idea at the heart of this is that without making it so you can craft any item or add any property at any crafting station, you can still require "special" crafting stations, but unify all the systems together into a single system that is consistent. Alchemical crafting, such as using the Stone of Change seems like it could be removed and just pulled into the Cannith system as recipes to clean things up. Things like Dragon Scale might have different flavors, based on which machine you use(if you use one that is controlled by different groups, you might get slightly different results), but the overall system would be the same, just different recipes or results based on the machine you used to make it.
Yes, SOME work would be needed here, but in cleaning up all of the different systems in the game, it would reduce the number of potential bugs.