One of the most underdeveloped parts of E:WoM is the minor Factions. The devs have stated that they want the world to be more alive and interesting and I think increasing the functionality of minor factions would really help this.
First of all I think they should all start with a random resource tile. That way they have something to trade for and so you have more reasons to conquer or interact with them. It would also explain why they live where they do.
I really think they should give out quests with improved relations being part of the rewards. This would keep you coming back every once in awhile. Also there should be several ways to gain control of them. You should be able to gain control my marriage, probably after a quest(rescue the princess/prince). Or simply save them from a rampaging ogre in another quest you have to unlock first.
Lastly they need more back story, when you first meet them they should spout some nonsense about being refugees and all their hardships. They also need more presence in the world. Right now they are to easy to kill. They should have a small army that scales as the game goes on. They should also have the ability to help you in war or whatever if they like you enough. If you do gain control of them they should also act as a normal upgradeable city.