Overall I'd love to see the Ottoman Empire, Byzantine Empire, and Austria ( Austria-Hungary). Though the area around Greece is already crowded ( 2 Greek Civs and Macedon) Constantinople/Istanbul would add two more Civs to the same area. The three empires I mentioned have had a huge impact on history and I don't see how they can be omitted. All 3 were in Civ 5 and Byzantium has a pedigree back to Civ III.
In Asia/Middle East I'd love to see a Jewish themed civ either Israel or Khazaria. I imagine Firaxis avoids it because of political backlash.
For Africa I'd like to see the return of Mali ( Mansa Musa). Also the return of Songhai would be cool too. And then maybe a Civ6 version of Carthage,Morocco, and South Africa..
For North and South America the native Civs in Civ5 and Civ4 were good. I'd like to see a return of Sitting Bull. Add in there Inca, Maya, Shoshone, Iroquois, and Canada.