Gonna give my two cents here. I have to admit, I didn't read the entire thread, its pretty long and brimming with interesting ideas. However, a few thoughts that jumped to my mind as I reviewed your discussion, tell me what you think.
Special settler unit (colonist) that is cheaper to make and probably has one more movement or something (while embarked and on land)
When its founded, it makes a city-state with random attributes. Also, give it a worker and a soldier? You get X amount of favor from it (something big, maybe 90 or something?). The favor degrades normally. Colonies founded near each other become part of the same colony.
The city-state does not give benefits until it reaches population 3 (like the maritime benefit does not trigger, this just seems more realistic, since a colony doesn't pay back from day one)
After Y amount of time (30 or 60 turns maybe? Civ V is big on multiples of 30), if you are still the highest in favor and still their ally, the colony becomes a part of your empire and you gain control of it like any normal settlement (or maybe it comes back as a puppet state, so you have the option to annex it or not)
If you are not the highest favor, and/or are not the ally of your colony, it becomes its own civilization.
If you have favor with another civilization's colony and it becomes its own civilization, you are in a certain diplomatic standing with it (If you are a 'friend' of the colony, you have a friendship pact when it becomes a civilization automatically. If you are an 'ally', you have a defensive pact when it becomes a civilization automatically). If the colony annexes normally into the parent civilization, your favor is wasted. You can gain favor like with any normal city state, with gold, spies, and through missions and whatnot.
Comments: I feel with the espionage system, and giving the opportunity for other civilizations to butt in on your colony, we can really capture the feeling of the age of Exploration, where Britain, France, and all of Europe were fighting for distant spots on the globe. Of course, you also have to make colonies worth it, and I think giving it that autonomy for the early stages of the city works well, along with the decreased cost of the settling unit and the increased movement so it can get to the far flung corners of the map. It saves on finances and happiness until the city has developed the surrounding area, etc.