For thematic and continuity reasons, we are focusing on a series of four dominant civilizations (Egypt, Israel, Assyria/Babylon, Greece) within their respective geographic regions (the Nile, the Levant, Mesopotamia, the Aegean), but Hittites will most likely be represented in some form in Part II as individual units within a parent Mesopotamian civ.'
The idea at this point is a succession of civs like this, represented in sequence for Parts I, II, and III:
EGYPT: Old/Middle Kingdom -> New Kingdom -> Late Period
ISRAEL: Pre-monarchy Hebrews -> United Monarchy -> Judahite Kingdom
MESOPOTAMIA: Sumer/Akkad -> Kassite Babylon/Syria? -> Neo-Assyrian Empire
GREECE: Minoans -> Mycenaeans -> Archaic Greeks
See above. Neo-Babylon was basically a successor of Assyria (although co-existing in a subordinate position prior to the sack of Nineveh in 612 BC and defeat of Assyria's last major resistance in 609 BC), and inherited pretty much their whole former empire. One of the titles of Nebuchadnezzar II of Babylon was "king of Assyria", indicating some form of imperial continuity. Since both the Neo-Assyrian and Neo-Babylonian empires took place in the 1000-500 BC timeframe, I chose the Assyrians to represent the Mesopotamian region, since they seem to have had the greater impact and influence, as well as much greater longevity. The Neo-Babylonian and Achaemenid Persian empires at least partly used the Assyrian models of administration and governance.
All that being said, I'm not ruling out a future Neo-Babylon civ for Part III, but that would have to wait until the main four civs are up and running.