I was thinking of doing the same thing but didn't want to begin work on this until after the patch is released.

The quickest and easiest thing for you to do would be to clone the Greek City States and use them as the model for the Aetolian and Achaean Leagues. No need to create new tech trees or units until you've worked out the kinks. To keep some balance you should try to have about two provinces for each league. The default map is a bit limited for this kind of mod though. USMCNJ's MoreCities mod is excellent and should give you an idea of how Greece should look but I think he went a little overboard with the number of cities he added to the map. Some areas like mainland Greece are simply overcrowded with provinces.

Technically Athens, Sparta, Syracuse, Pergamon and Rhodes should all be their own independent states with no relations to either league.

Good luck!