While I was not asked (forgive my notorious lurking/commenting, y'all!)
I would like to enhance your idea, Thunderbrd.
The concept of using a Great General as an attached unit
or as a Great Gommander could very well be adapted to the missionary, trade merchant, judge, storyteller or even an "inventor" as well:
While you could either use the unit for a simple mission with big benefit (like the ambusher +100 spy points or the general attached to unit 30 xp) you could also get slow benefits if using them continously.
- The Merchant (max 1 per 5-10 cities) could either receive a large lump sum like now (action: "sell all assets and retire")
or receive a small lump sum when he arrives in a new city - as well as a little xp.
The city he visited the last time will give not reward him again if he leaves and re-enters.
At first, the Merchants yields will not pay off its maintenance costs he produces while travelling between cities, especially in own territory where the yields would be lower.
But each trade also gives xp and at some time the promotions he gets would let him spot certain opportunities where to make better deals and have larger benefits. A new property supply and demand could be needed to be introduced for this perhaps.
(This suggestion is inspired by the board game "Merchants and Marauders" which I gifted a friend recently)
Some civics would standardize the yields of merchants (like socialistic one) others would have big difference of margins (profit) between the missions and also a chance for the merchant to "die" (to go broke).
Some very experienced merchants could also build banks and receive promotions that are acticve in combinations with certain civics, like corporate and federal,
preventing them from being percecuted for fraud and going broke
(the "too big to fail" [or "TINA" {there is no alternative) promotion comes in mind (civic: mind control^^}]; upon picking it for the merchants -2 
in each city until change of civic^^ ah well people tend to forget, let half of it expire after 150 turns 
)
if used on foreign cities: "our trade relations have been fair and fruitful" attitude modifier slightly effected, + small amount (0.x) of xp
- The missionary could have low autoconversion chances (promotions for increase) and could
maybe have influences on the leaders of foreign countries. So if you had X amount of missionaries in the enemies cities their attidude modifier we are angry that you have a different state religion would rise to a certain amount until it lowers again. You could subdue a country this way -- much like the christians did with viking religions.
If not used for slow and strategic use they could still do their original "convert" mission.
- The storyteller would either have a significant amount of culture at once
or, if in a city, be able to spread steady culture - less first, more with promotions. and also influence the attitude modifier of foreign nations "Our people are impressed with your achievements". Needs new cities like merchant for next xp/culture gain.
- The inventor could either give an one time amount of hammers or science to a city
or be used to steadily work as a development aid worker (in own lands +hammers in exchanging cities, similar mechanic like with merchant; effect in foreign nations: creating a chance to increase the "you helped us" modifier over time (which also slowly autoreduces!).
XP for promotions of course would be given for each turn it actually influenced the modifier
- Regarding the Judge I don't know I guess you already have concepts
For the Rogue or Ambusher or Spy I liked the "pick up rumours" action in cities.
The rumours would be like little events/quests, good and bad, giving xp upon success to verify them
(like: "in the tavern a old drunk man tells your rogue xy of a treasure he once hid somewhere next to city xy. if you look for it and find it (walk on that tile while on this quest) you will be rewarded nicely (xp and money)"
---> picking up rumours costs a lump sum (because in this case you had to fill up that ol' bastard to loosen up his tongue
)
As not all rumours are true you very well might search forever and find nothing so you could also disband rumours and pick up new ones with your units. Only one rumour could be active at the same time for each civ.
(also inspired by Merchants and Marauders)
(And this one is updated for the AI to understand its value as well.)
