This is kind of an amalgamation of posts I've made in other threads, but it addresses a significant problem in a fairly simple, easy way.  The problem is that NPC's, while numerous, are not particularly useful, and not really an enjoyable part of the game. You don't really get attached to them, and they all seem pretty much the same, while the ones out wandering around seem pretty lifeless.

Right from the start, there should be lots of champions.  It takes an exceptional kind of person to survive a catastrophe like has overtaken the world, and quite a few of them should be out and about seeking to profit, survive and better themselves just like you are (just smaller scale, without the magical ability). I think the problem with the current system is that right now they 1. don't do much for themselves, and 2. don't have enough out there to do (to impact the world in general and your nation in particular).  Couple of ways to solve this problem.

First, have champions do more, whether they work for you or are just on their own.  That merchant out there, who nets you two gildars a turn if you hire him, should be trading between cities, carrying stocks of food, ore, weapons, ect in between cities and outposts (more later) and selling them for a profit.  He should have his own money, and have the amount of goods and money he makes increase based on the number of trips that he makes.  Everytime he comes into a city, the owner of that city gets a small sum (dependent upon the size of the city and the level of the trader) in tax revenue from what he sells.  Initially he'll be alone and small time, but as the amount of money he has and makes increases, he should eventually hire guards to protect him and his merchandise.  This is not a hired hero. This is him, acting on his own, out in the wild.

If you hire him, you should be able to do the same thing, the only difference is now you choose.  Govern a city?  That city gets a bonus to its income (which increases the more turns he spends as governor).  Put him on a caravan route?  He acts as a better caravan, and gradually improves at that.  Or just have him in his nice safe market in your city?  He nets you the two gildars (or however many he does based on his level) per turn that he does now.  But that should be the least profitable of the options, since it is the safest.  He should charge you a salary though, which increases the better he becomes at a given task.

That thinker, who nets you two research points if you hire him, should be able to increase research by a net percentage if he is governor.  Or he should be able to manufacture special equipment, giving you better and unique items in your shops.  Or you can put him in one of your libraries, and he churns out two research points.  But once again, that should be the least profitable of the options.  On his own he should be a freelance artificer, making items (better than what you can produce generically) and selling them to anyone with money.  If he gets rich enough, he can create a little inventors cottage, which can be the source of quests and new equipment.

The administrator.  I see these guys as businessmen (as distinct from traders).  They go around developing undeveloped resources and offering business propositions.  You would see them running a little mining outpost over some ore (which the above mentioned trader could trade at, or you could trade at), conducting a little hunting operation around some wild game, running a clay pit using a bunch of slaves (would be a fallen administrator), offering to set up a small business within your territory (say an armory or inn) which nets money, ect.  As they continue operations and continue to sell their wares their operation increases in size and sophistication, increasing production (and protection).  Naturally once your city has grown up to the resource/building they are using, they will have to be amenable to a "friendly, in no way hostile and in no way influenced by the 200 archers we have nearby" takeover of their operation for a certain amount of cash, or you can just allow them to continue operating independently.

The mercenary could really go one of two ways.  As part of a band of "adventurers for hire" they could offer their services in clearing out lairs, taking on missions or quests, ect.  Or as a mercenary NPC (possibly a couple) with a small band of soldiers they could hire themselves out to people in exchange for certain amounts of time for a subsantial fee up front (based on their level and the quality of soldier they are bringing with them) in addition to a small "replacement fee" every time one of their soldiers dies.  This would provide you with incentive not to wipe them out or be completely suicidal with your mercenaries (and saves the trouble of a "relations tracking system").  As time goes on they gain experience from fighting (leveling their character up), and money from contracts and "death payments" increasing the number of soldiers in their band and the quality of their equipment.  If they get big and rich enough they can establish a fortress in the wastes, or in some welcoming kingdom (who then receives a discount on their services), and operate out of that (missions and quests can be both recieved and given from said fortress).

And finally the adventurer.  This guy operates out of wherever he can find a secure base, and goes to where the monsters, ruins and adventure are.  Now at the start that is pretty much all around.  As time goes on and the wildlands recede, adventurers would begin to congregate more and more around the remaining wild areas.  Adventuring in populated territories would have to be largely centered around interactions within your empire (criminal underlords, cults, banditry, ect), and support a lower density of adventurer.  These guys would get most of their money by exploring lairs, ruins and dungeons, killing creatures, and taking assignments from players.  They would spend it on better equipment, lodging and supplies.  Eventually (after they hit a high enough level) they would pay for some kind of stronghold (perhaps one of the lairs or ruins that they clear out) or request permission to build a mansion/house within your territory.  This would be a source of quests, and occasionally you would be able to bring them out of retirement for a certain task (like fighting off an overwhelming invading army).  The more adventurer friendly you are, the more would be inclined to settle in or near your territory, thus giving your more potential in that regard.

However, there needs to be lots of champions to see development like this, because for each freelance wealthy merchant, knowledgable sage, powerful mercenary or successful adventurer there are 10 more lying dead in a ditch somewhere.

Which leads me to point number 2.  There needs to be more lairs, creatures, and things to do especially within your territory.  These NPC's that are out doing their class job need something to do (in the case of adventurers), or some risk to them (in the case of traders, administrators and thinkers).  There needs to be a dynamic here.  If you are really good at keeping your nation and the area around your nation swept clean of threats, you should have a lot of traders and thinkers and administrators rolling around, because there are a minimum of creatures out there killing them.  That being said, you will have fewer adventurers, simply because there isn't a lot of lairs to explore or creatures to kill.  Mercenaries will go where the money is, so if you are at war or have a lot of problems with monsters, then you will probably see more mercenaries wandering around looking for employment.  This is a pretty easy dynamic.  If you've got a ton of monsters running around, traders and sages are going to be killed about as quickly as they leave your borders (or in your borders), so there won't be that many of them.  When they autogenerate, they die.  If things are relatively safe in and around your territory, more of them will survive to the point where they can actually defend themselves and become productive.  Adventurers on the other hand, will go where there are a lot of lairs and monsters around, and where there are facilities to support them  It shouldn't be that difficult to program preferences like that, nor difficult as a player to support various buildings for assisting various types of NPC's.

Right now the problem with champions is that we don't have a "living world."  They just kind of wander around not doing a whole lot until they get hired.  Really, we shouldn't be able to hire most of the NPC's (wage costs are probably a good limitation here).  Most of them should be going around doing their own thing, but continually influencing the world around them and your nation.  Once they actually do that (if they do), then the problem should go away.