First suggestion: Unlock Web
Along with the skills/perks tab, the unlock web could be a section that allows you to chose a path you want to go down in the game. (Ex. Tinker, being able to mash up different parts on things you otherwise wouldn't be able to, alloys.)
Second suggestion: Alloys
Being able to alloy metals in the smithery or some other place and then sell that off to your customers, making a better material in worth than the number of metals that you combined, or equal in worth but just looks really cool to you. I would suggest it to be a unlockable thing in the web relative to the worth of the metals you alloy.
Third suggestion: Shop expansion
Expanding the shop would allow for you to put stuff that you wouldn't have been able to. Like if you just had the basic shop areas (The one you start with right now, or smaller) You wouldn't have the correct area to place a smeltery or a storage room for ores that you collect.
P.S., I love the game! I love games with vast customizable options throughout the game!