First of all, thank you for making this amazing game Moon Studios it’s definitely one of my favorite games ever!
Now here are some suggestions based on my experience so far:
Rune crafting: weapons are sparse, and you can’t always equip a weapon to see what it’s rune special does due to stat limitations. Or, if you find a good rune and put them all on your favorite weapon. But then you find a new cool weapon and want to put the same runes on it. And don’t have the runes to do so or can’t farm the weapons that have those runes.
Rotating Shop Inventory: personally, I don’t like the static shop inventory. I would like to be surprised every time I visit a shop to see something new. Or have the chance to buy a piece of gear/recipe/component that I wasn’t able to farm. This can be especially helpful once the world hits a new tier, and you can’t farm the previous tier for the gear you wanted but never gotten; you could make a new realm but if it’s one of the later tiers it requires more and more time. Also, an option to pay X resource to refresh the shop again.
Realm difficulty: normal, hard and custom. I personally liked the durability system on release. It made me play safer and when I put the repair rune on another weapon, I felt like I overcame a hindrance. Also, some people have limited time and might not be able to farm a lot of resources so custom drops might be helpful to those.
Dismantling gear: dismantle a piece of equipment for resources or a recipe. My favorite weapon is a halberd. So, I was super happy when I found the Regal Cleft. However, I then put an ice enchantment on it, and it rolled the minimum value (it also didn’t show the ice enchant (bug?)). I don’t mind farming resources to try it again until I get a better roll.
Dye system: the art, gear, weapons everything is visually stunning. We can already personalize our gear and enchants. But it would be so awesome to mix and match different set pieces and have them look similar. Maybe I want to play as an assassin wearing an all-black outfit, or a knight in shining silver armor with blue and white fabric. Different fabric/armor dyes or even patterns would look so amazing and allow the player to further customize their character and express themselves.
Barber: an option to change appearance in game.
Romance: we can buy a house in Sacrament and fully customize it. However, every time my Cerim comes home from an adventure no one is waiting for him 
The home is where the heart is. Some small and simple affection system would suffice, something like Stardew Valley. Maybe express interest, meet them in Caroline’s tavern and then gift them their favorite gem from the enchanter Eleanor and put it on a ring or something. And when they have moved in, we gain a daily bonus like a homemade meal for our adventures; and some banter 
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Edit: spelling