For crafting, i would suggest one simple thing - make smiths and armourers manufacture variable level weapons, instead of fixed. This way, player would be rewarded getting access to Master smith or armourer by being able to get Master level items with high level stats, while Journeyman and amateur would only create lower level stuff.
Also, there should be some way to reforge existing equipment/weapon to higher level version. Just make it consume additional resources and money, so player would be able to increase the level of his equipment instead of throwing it away or dismantling it. There is a lot of people who like the initial Wolf school armor, but that armor gets totally obsolete within prologue so there is no way somebody could wear it later. With ability to improve armor level, player would need to search for high level armourers to increase the level up (let say amateurs would improve it up to level 8, journeyman could do it up to level 12 and Master could do it up to maximum level (based on actual character level, so master armourer would be able to fit the armor to current level for a hefty sum of money)..
Same could apply to weapons as well, so if player finds a Moonblade level 1, he would be able to reforge it for higher level instead of throwing it away or selling it immediately when he finds it. Instead, actual custom effect of those weapons would be much more important, while base damage would scale based on weapon level..
for alchemy, i have few suggestions - most important is to greatly reduce amount of Dwarwen Spirit loot in the world. There is just way too common, so player practically doesn't need to buy it at all... Alcohol should be also a bit costlier, so player is forced to spend his money on it.
Another thing that could go with alchemy would be cooking - just make some cooking recipies so player can roast all that raw meat into roasted meat or something.. plus, it would be a good idea make fresh meat become rotten over time, so hoarding a ton of fresh meat would be relatively pointless.
and third - one idea with decocion potions - what about making them nonrefilable, but instead having let say 10 doses. This way, some very powerful potions would be restricted to 10 uses thorough the game, so player would have to decide when he wants to use them, instead of repeating certain pattern over and over before every battle.