Yeah, I agree that a Cahokia city-state and a Choctaw full civ is probably the best alternative to a full Mississippian civ. I would hope that Quigualtam and Tuskaloosa (within the spectrum of the last leaders of a civ) would've been closer to Cleopatra than Romulus Augustulus but until we find out more somehow it doesn't appear likely. I'm still looking up more on him but so far Zutacapan from the Acoma Pueblo also appears to be in a similar standing. For what its worth, Quigualtam did send some pretty sassy messages to de Soto and attacked his expedition with canoes so I guess that's something but I'm not sure if that on it's own is enough.
Overall, I just find it to be such a shame that the Mississippians and Puebloans don't seem likely to make it in the game. Native North America (north of Mesoamerica) is still struggling to even have a regular staple in the series so it's quite a blow to lose out on 2 civs that, if they could be included, virtually no reasonable person would question their worthiness as civs. Outside of them, even the most notable, settled, and powerful Native American tribes seem to struggle to be seen as 'worthy' of inclusion even by some on these forums let alone the larger gaming community and Firaxis itself. I'm glad that we have the Cree and it seems likely that we'll get at least one more in another expansion. However, assuming that the second one is another new one like the Navajo, etc., it starts to imply that Native North American representation in the game is like a ferris wheel where even the Iroquois have to cycle in and out of games instead being a staple right alongside America and England.
I'm aware that Africa and Polynesia also suffer from lacking in representation of their strongest nations, but it seems to me that Native North America (and similarly Native South America) not only has the least representation but also struggles the most to be recognized for and have any solid staples from game to game.