With the exception of the Hittites being dropped in the transition from III to IV, the civ franchise up until V had never abandoned a civ; with every installment all civs from the prior game were either brought back, refined into a more specific concept (see HRE/Austria, Vikings/Denmark, Polynesia/Maori, Celts/Gaul), or replaced with a comparable substitute (see Mali/Songhai, Khmer/Siam, Denmark/Norway, Austria/Hungary).
At the moment, we have only three slots left in NFP, but five civs which have not been returned, refined, or replaced:
* Portugal
* Venice
* Morocco
* Assyria (Sumeria presumed to replace Babylon atm)
* Shoshone (Cree/Canada presumed to replace Iroquois atm)