Using different leaders for the same civ in order to represent wildly different political bodies over the same territory is genious (Constantine of the Romans in order to represent Byzantium, Charlemagne of the Germans in order to represent the Holy Roman Emire, etc), but that might not be enough to account for the huge differences between some of said entities (I don't think that Mhugal India would be different enough from "regular" India with just a Unique Leader, seeing how little difference there is between Gorgo VS Pericles).
As for the inclussion of polemic civs such as Tibet or Israel, I think that the safest option would be to go with the "city state route".