If you are a merchant, a new personalized faction system for the people buying from you. Maybe the Holy Nation hates you, but John the bartender will let you hideout in his basement because you're his best customer and have a high reputation with him.
Maybe the thief guildmaster hears you are locked up, and stages an escape (with player confirmation that's what they want). Maybe you need something, and can put in an "order" with the local fence.
A couple things I would like to see in the new game, is expanded playstyles. For instance, if we are an armorsmith, we need more clients to sell our armor to. Perhaps you could supply one faction or another with goods, and become friendly with them. Perhaps this would cause another to become angry with you. Perhaps you could be a black-market dealer and sell to both.
I think if you have a shop counter, you should need someone to run it. They should have a haggle skill, and try to upsell customers. Sometimes it works, sometimes not. Give them the ability to compromise and come to a deal.
I'd also like to see a shop counter where you could set up "buy orders". Put money in the bench, along with stuff you want to buy, and traders will sell it to you.
Although some people would probably disagree with me, I'd like to see fewer "random" raids when starting an outpost, and then increase in intensity as you have more people living there or some other metric. It would be nice to be able to start out in a single tent/building with nearly nobody bothering you, so you don't immediately get overwhelmed and die. Then as you get more houses, and more people, bigger conflicts. Perhaps it would be better if you could work out a deal with the "hungry bandits" and feed them, or pay them to leave you alone.
I'd like to see more recipes available / for trade / sale.
Animal breeding.
More types of ore for building out of. Rare resources only found in hostile locations. Getting that Mithril will be difficult, but if you want the best weapons, that's what you need to get! Maybe you even need to take over an NPC outpost to get it!
Lumberjacks. Not sure why you don't have this already. Wooden weapons. More advanced wooden/metal weapons.
Automated trade routes set up by the player. So, if I want to send 50 food cubes to CityX, every week I can set that up (assuming they are willing to pay... if relations are good. IF not, maybe they double cross me. Maybe i could miss a shipment to starve them on purpose. Maybe the traders get attacked by bandits on the way. Maybe I could pay mercs to go with them.
Ways to wage war. With my previous suggestion above with the armor, armies have need of gear. IF you are supplying a faction, and they are better equipped than their enemy, maybe you could entice them to go to war. Maybe you could set up your own NPC army with recruits to send into battle. Maybe you can do this, and I just haven't gotten there yet.
Easier ways to recruit people. If you have an outpost, there should be a chance an NPC wants to join you, and will randomly show up and ask. Accepting them could cause disfavor from another faction if they are wanted, etc, or maybe they are just looking for some honest work and will join you for free. Maybe you have to pay some, if they have skills you're looking for.
Anywho, just a couple things I've thought of along my journey so far
Hope you enjoy and can use some of them!