my bets:
1. Portugal
2. Sioux
3. Bantu ( I'm almost sure they gonna join many african cultures, included Zulu, in one single civ)
They almost certainly won't - that would be a reversal of the Civ V trend to get away from Civ IV's lumped-together civs like Native Americans and Vikings and replace them with named states. They've only made exceptions for the Polynesians, who can't readily be incorporated into Civ any other way, and the Celts, who have a precedent for being in Civ. It's very unlikely they'd take a pre-existing, named civ from a previous game and incorporate it as part of a generic ethnic group.
Besides which, Shaka wouldn't be a very appropriate leader for the Bantu generally.
I seriously doubt that Mali was planned from the start, let alone that the reason for Songhai spellings was that.
I don't expect they planned that they necessarily would have a Malian civ, but since it was in a past Civ game they may well have decided to leave the option open from an early stage. The fact that they later used the Great Mosque of Djenne's conventional spelling (and didn't correct the spelling of the Songhai name) suggests that the choice of unconventional spellings for the Songhai city names was deliberate, and it's difficult to think of any other reason why the Songhai would be singled out for deliberately misspelled cities. Those don't appear to be either Malian or French spellings of those city names.
Fall of Rome: Byzantines, Huns, Celts
Into the Renaissance: Austria, Byzantines, Celts, Netherlands, Sweden, Spain
That's 7/10 of the civs related to the scenarios. The only ones that weren't (Carthage, Ethiopia and Mayans) had something to do with new mechanics (Melee naval and religion respectively)
I'd forgotten the Celts were in either, but since neither scenario should logically have had the Celts involved, I suspect they were added to the scenarios because they were there rather than either the civ being selected because of the scenarios or the scenarios being designed to fit the civ. Although the Celts do indeed fit the expansion's religion theme.
I'd also forgotten the Netherlands altogether.
Spain of course doesn't count since it's a pre-existing DLC civ. Still, I have to concede that you have a point that the majority of civs were indeed involved in the scenarios.
Though as for the remainder, it's a bit of a stretch to describe "naval" as a core G&K theme, while the Maya aren't particularly focused towards religion merely by virtue of having a bonus to their faith building (the science boost is the key selling point of that). While none of the new civs got any espionage-related abilities.