I agree with most of my fellow RTW players on most everything (representation of all cultures, use of "buffer" factions would be a plus, strong spread of possible alliances) except for the Greek pieces. At the time of Rome's ascension to power, Greece was mainly divided into, as one of you mentioned, the Achaean League, the Aetolian League, and Sparta (gotta love the Spartans). Then there was the dominant force in the north that was Macedonia (duh).
I don't believe there should be a "Greek Cities" faction...I love the idea of starting the game with the Achaean and Aetolian Leagues along with Sparta as an independent faction. Of the free parts of Greece (south of Macedon), the northern sector was controlled by the Aetolian League (mainly Athens) while the southern sector was owned by the Achaean League (save for Sparta, of course). Each League would start with 2-3 cities; I've done a little bit of research but am still confused as to which MAJOR cities lie within each league besides Athens in the Aetolian and Corinth in the Achaean. Also, from what I can tell, Kydonia (Crete) joined the Achaean while Rhodes was with the Aetolian which gives each League a strong island presence away from the mainland. To me, that would be interesting - have the Aetolians (Athens and Rhodes), Achaeans (Corinth and Kydonia), and the Spartans occupy the non-Macedonians sectors of Greece to begin the game. Each would have their own sigil and so on and so forth. Throw in Syracuse and Pergamum as allies of Achaean and Aetolian, respectively, and you have party.
However, my main idea would for what happens if you join together all these cities. If you start as one of the Greek factions (Achaean, Aetolian, or Spartan), you would have the option to create a whole new faction with a new sigil and name called "The United Greek Cities" or something to that respect, if you conquer all the required cities. You would gain the advantages each may have (access to Spartan Hoplites, technology, etc...) by forming this new faction. This would be a more advanced version of what one could do in the Medieval Total War II Teutonic expansion where, if playing as Denmark, one could form a more powerful "Union of Kalmar" after gaining certain Scandinavian cities and killing the King of Norway. Denmark, now known as the Union of Kalmar, gained access to three new units and raised a different sigil.
When playing against the Greek factions, however, the union would be formed after a certain number of turns if all the pertinent cities still remained under control of the three factions in question. This would make it important for one, if playing as the Selucids, Macedonians, Romans, etc... to take at least one of the cities early so as to prevent the permanent alliance later on.
While it may be out there, I like to think it's still in the realm of possibility. I've always been a huge fan of the Greek Cities faction and would like to have more options when it comes to selection and eventual expansion.