Okay, probably a good time to summarise what we know.
We have 5 confirmed civilizations of the 9:
1. Poland
2. Assyria
3. Brazil
4. Zulu
5. Portugal
Beyond this we know that they wanted to add Pueblo, and it's unlikely that whoever they chose instead wouldn't being a Native American civilization. In such a case we can, for now at least, assume that the most likely next Civilization is something like a Sioux Civ or another Native American group. The reason for mentioning Sioux directly is that they've been in the game before. For now:
6. Sioux or another Native American civ
Beyond this we have another 3, and we have hints from the city states. As in the first post, we have already account for some changes, but we still have one militaristic city state and one maritime city state unaccounted for. At this point the best guess to make from here is that we can infer the possibilities for 7 and 8 from this. The city states that may have been removed from the militaristic city state list are:
Almaty
Budapest
Hanoi
Sidon
Valletta
From these the most likely would seem to be Almaty with someone like Timur, Budapest with Hungary or Hanoi with Vietnam. Being European Hungary certainly would be a good shout, but with a good chance of female leaders Vietnam is one that really could stick out. I'm going to guess that Malta is not in, but who knows... I could also mention Phoenicia here, but I'll get back to this point. In any case:
7. Vietnam / Hungary / Timur / Malta...
Past this is the Maritime City states that are as of yet not confirmed to be in the game:
Jakarta
Manila
Mombasa
Quebec City
Ragusa
Sydney
Venice
Of these we can effectively rule out it being Mombasa being removed as a Swahili Civilization without Zanzibar (which has already been seen in BNW screenshots) seems very unlikely. I also doubt that the Philippines are really an option, but again, you never know. Croatia is at best a very outside chance, however it may be linked to Venice, but like Phoenicia, I'll get back to this point. So that leaves us with Indonesia, a prime candidate to many, Canada and Australia. So again, as before:
8. Indonesia / Canada / Australia / Croatia / Phillipines
So, there's also three interesting cases now:
1. Phoenicia - Sidon and Tyre (Militaristic and Mercantile)
2. Venice - Venice and Ragusa (Maritime and Maritime)
3. Italy - Venice, Milan, Florence and Genoa (Maritime, Cultural, Cultural and Mercantile)
The interesting point here is about the number of city states replaced. The current distribution of unknown city states doesn't exactly follow these as of yet, but it could. For the sake of reference, if we are at a point with the following, we can guess:
1 Militaristic and 1 Mercantile - Phoenicia (Likely)
2 Maritime - Venice (Weak)
1 Maritime, 2 Cultural and 1 Mercantile - Italy (Very strong)
The brackets here reference how strong I feel it would be should we see those numbers of unexplained city states from here. That is, a militaristic city state and a mercantile one would be quite indicative of Phoenicia, but it could mean two other city states becoming civilizations or some other combination. On the other hand having 2 unexplained Maritime city states (we have one currently) would only being weakly indicative of Venice, and could mean a lot of other things, even... ugh... Canada and Australia... Finally, should we see 4 unexplained city states with the combination mentioned for Italy, it would be pretty much a finger print, if we saw that, it would be almost certainly be Italy, as no other Civilization could replace that many, and so many unexplained new city states would be a strong indicator here.
I'd also again point out that Ragusa is the Croatian city, not the Italian one, although it was intially called the Italian one in the game, that has since been amended (in a patch for Vanilla if I'm not mistaken).
Finally, the point of Mbanza-Kongo. Whilst we don't know what kind of City state it is, we do know that the city is (and was) a religious and cultural centre for the region, far inland and not on a major river (that is, it is not a port). As such the best guess is that it's either a religious or cultural city state. From this we are left with the following options for what it could replace:
Lhasa
Vatican City
Brussels
Bucharest
Florence
Kathmandu
Kuala Lumpur
Milan
Yerevan
Of these, Kuala Lumpur (which from what I know was only founded in the ~1850s) can be ruled out almost immediately, as a Malay civilization is extremely unlikely, especially if Vietnam or Indonesia are in. Nepal and Romania can also probably also be ruled out as well. I doubt the Vatican or Papal states is in, but you never know. Past this we have Tibet, which certainly would be an interesting inclusion, but I still don't see it happening for obvious reasons, although there is a chance. This leaves Belgium and Armenia as the likely candidates, although this could also connect back to Italy, but that's much more complicated as discussed above. So:
9. Belgium / Armenia / Tibet / Papal States / Romania / Nepal / Malay
To repeat the point, Phoenicia, Italy and Venice are all still possible, but the mix of city states (as mentioned above) is still not indicating that. That said, if Mbanza-Kongo is cultural and another Maritime and a Mercantile city state show up, Italy would almost certainly be a new civ. From what we have currently though:
1. Poland
2. Assyria
3. Brazil
4. Zulu
5. Portugal
6. Sioux or another Native American civ
7. Vietnam / Hungary / Timur / Malta...
8. Indonesia / Canada / Australia / Croatia / Phillipines
9. Belgium / Armenia / Tibet / Papal States / Romania / Nepal / Malay
We can also, based on city states seen so far, rule out:
Olmecs
Israel
Czechs
South Africa
Switzerland
Slovakia
Kongo
Latvia
Sumeria
Bulgaria
Panama
Serbia
From the list, my best guess at the time would be:
1. Poland
2. Assyria
3. Brazil
4. Zulu
5. Portugal
6. Sioux
7. Vietnam
8. Indonesia
9. Belgium
Here I would imagine Buffalo being the resource that has not been named, but it could be a number of things and could have a number of implications as mentioned elsewhere. From the city states seen though, that would be my best guess, we'll see though.